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A +1 keen long sword is the equivalent of a +2 weapon. Holy is the equivalent of a +2 enhancement bonus. Therefore, adding holy to that weapon would make it effectively a +4 weapon. That means they must pay the difference in cost between a +2 and +4 Weapon.
Also, they need a caster high enough level to make the weapon who has Craft Magic Arms and Armor. You determine how available those are. I typically don't let my players find anything better than a +1 weapon anywhere but a big city.
Also, note that enchanting the weapon is going to take a LONG time. 24 days for the example you provided.
The COST is half the market value, but the crafting time is full market value. So it costs 12,000 gold, but it takes 24 days since the market price is 24,000 gold.
It costs the crafter 12,000gp but we're talking about a player paying an NPC to do it, which would cost the player 24,000gp.
Also, the craft check is damn easy (CD 5 + Caster Level). So to low level items, isn't impossible to the crafter to add +5 on the CD to halve the craft time. To higher level items there's some risk. You can the offer the PCs the bargain: relatively "safe" but slow craft, or take some risks and get the item earlier.
Depends on the size of the city. This page gives some guidelines:
http://paizo.com/pathfinderRPG/prd/mastery/settlements.html
For your example, to upgrade the weapon you'd still need a wizard capable of building the weapon from scratch. A +4 magic weapon costs 32,000GP. Checking the tables in that link, there is no settlement size that has that as a base GP item. So I'd say no, there's no way to upgrade the weapon to that.
Now, let's say they want a +2 weapon (equivalent), that's 8,000gp so any settlement of size Large City or bigger should have a 75% chance of doing it.
(Other games have stats or random rolls for the NPC class and levels a settlement of certain size would have. I'm not aware of that for Pathfinder.)
There are rules for whats available at hand in large cities, but if they are willing to wait to have it crafted (which can as mentioned take days) then they should be able to find it anywhere there is a signficiant wizard or cleric.
My opinion is you should in some way make gear available that your players want within the appropriate wealth constraints. Whether that means placing specific treasure in the adventure, having a caster to be hired to craft or having a magic mart, you should offer them SOME avenue to this. Which one depends on you.
Its one of the reasons I despise how magic item reliant the game is. It takes control of the world and story away from the dm if he doesn't want to handicap his players.
Quick vet DM/GM advise: decide before the players go “Magic-Marting” (ie buying whatever they see in various books as their PCs) how you want your campaign to roll out with the availability of magic items and NPC crafters.
If, like most grognards, you envision every magic item as its own special snowflake the ready availability of crafters may rapidly cause you to reconsider how you are going to be able to tell the story you are trying to tell.
On the opposite end of the spectrum, having the expectation that there’s a magic version of Amazon.com (“just cast sending or whispering wind from these convenient locations with your order details!”) can also be off-putting.
If you’re new to game mastering, this is doubly important because you’re establishing patterns in your GM style and expectations in your players and you may find it more difficult to retrain both yourself and your players later.
3 main considerations to your specific query:
If the characters have a time constraint, they will not have time to wait while their weapons are upgraded. It generally takes 1 day per 1,000gp base (sale) value of the item. Do the characters believe they have this much time? Do the players believe they have this much time? Do you want them to have this much time? How does this fit into how you envision your campaign taking place? This may be an excellent time early in their careers to establish some verisimilitude and have something come up while the characters are waiting for their items to be crafted and force them to choose to go on an adventure without their better gear or lose a plot hook or the good will of their allies.
If the players are in a metropolis like Waterdeep or Absalom, odds are they will be able to find someone who can craft for them at a reasonable price. If the players are in back woods area where the price of their +1 weapons are about the value of the town that they are in, it may be far more difficult to find someone that they can retain to upgrade their weapons.
To upgrade a +1 keen longsword to a +1 keen holy longsword is 24,000 gp and requires a 7th level good aligned divine caster for the holy part and a 12th level caster in order to upgrade a weapon to +4 and 24 days of work. Is there someone the PCs can hire to do so, who is willing to give up effectively a month of their life in the area? Depending on your plans for the campaign, this may be an excellent way to “hook” the players for future encounters or smaller encounters. If your players are relatively new as well, they may not be bored with the trope of “I will be happy to make you your magic, but first I need these rare components found in the dark wood to the north”. This is an excellent vehicle to give the players the sense that they are having input in the direction of the story, as well. Encounters will occur because of actions they initiated, giving them a bit more “buy in” in your game. Of course, if you already know that your game isn’t heading in this direction and you find the upgrade of weapons should be handled in a far more mundane manner, there’s always the “travelling pilgrim” who may be able to help them out in exchange for a donation to the local temple in the amount of their upgrade cost.
Hope that helps.
-TimD