That's up to you to decide. Here a few things to think about though.
At high levels you really have PLENTY of spells. More than enough to get you through the day if you memorize the right ones, and if you don't that's what scrolls are for. While more spell slots is generally better, having more than you'll use is just a waste.
There are a few spells at 9th level that are game changers. Time Stop is one. Wish generally isn't worth it because of the cash investment, but Miracle certainly can be.
Here's the big one and why people generally deem Mysthic Theurge to be a trap. If you are creating this character at 8th or 9th level it's not a bad proposition. Being a 3rd level Wizard, 3rd level Cleric (or whatever else combination gets you where you need to go) at 6th level is pretty awful. 2nd level spells at level 6 and 7? You can't keep up with the challenges put to you. This disparity in power (yours vs. that of challenges you encounter) is lessened as you level as a MT, but you'll always feel you're right behind the curve and nothing you can do about it.
It depends on your playstyle. If you want to be a healer/buffer then being a couple levels behind is probably okay, and the extra spells can be a boon. If you're the only healer/arcanist in the group however your party is waiting entire levels before they are able to raise dead/heal or teleport for example, which can really hurt a campaign.
From a sheer optimization standpoint, I imagine the response is unequivocally, "No, it is not worth it to give up ninth-level spells." Ninth-level spells are pretty good, especially the ones you mentioned. Some encounters might go so far as to almost require them - Disjunction or Mass Heal come to mind.
You may have a different experience, though. I, for one, think I would have fun casting tons of 7th and 8th level spells, two at a time.
Just about any 20th-level character could be fun to play, however. The game is in getting there. A particular difficulty with the Mystic Theurge (that may not be obvious until you play one) is that there is a good stretch of time during which they're just not very good. Assuming Cleric 3/Wizard 3, then Mystic Theurge, you gain 3rd-level spells at level 8, and 4th-level spells at level 10. By then, you're starting to look okay, through your sheer number of spell slots, even though your wizard and cleric friends are casting Teleport and Raise Dead. You don't get Heal or Disintegrate until level 14, long after they are needed.
Basically, don't complain when you're a 7th-level spellcaster whose best spell is Scorching Ray.
Is it worthwhile to give up 9th level spells for having a ridiculous number of lower spell slots via Mystic theurge?
A Cleric5/Wizard5/Mystic Theurge10 has full casting progression to eight level spells, can swap spell slots to an extent, and at level 20 can cast two spells in a round. shazbot!
But is it worth giving up wish, miracle, gate, etc.?
That's one way to approach it. . . assuming that level 20 gameplay is what's important to you. Most of the time you're not level 20. If you're talking about building a character to progress from 1-20, MT has some pretty significant drawbacks versus regular casters.
The biggest issue is that you're behind when it comes to caster level. Assuming you're not taking 3.5's Practiced Spellcaster or similar abilities (like the magical knack trait), spell resistance is going to be a pain. There are ways around it (even the new Piercing Spell feat works), but it's a problem you have to work around.
You also have to deal with the fact that you're casting spells at a lower level than expected. At 7th level, you're expected to cast 4th level spells as a cleric or wizard. At Cl 3/Wz 3/MT 1, you're casting 2nd level spells. The MT is one spell level behind a sorcerer. . . and a lot of people can't stand that about sorcerers.
There are ways to approach the MT that make it a strong choice -- but it's not for everyone. I think it's pretty balanced.
That's one way to approach it. . . assuming that level 20 gameplay is what's important to you. Most of the time you're not level 20. If you're talking about building a character to progress from 1-20, MT has some pretty significant drawbacks versus regular casters.
Seconding this. MT looks pretty good at 20, but what are the odds that your campaign will get that far? 0% of my 3.X/Pathfinder games have.
And MT is a whole lot of suffering most of the way to get there. Suffering for you, in that you're the weakest member of the party, and suffering for the other players for having to keep your dead weight ass alive.
As you get into the teen levels it starts to get okay, if you don't mind mostly being a buff-bot for the rest of the party.