Do as it says... you cannot deny the blade... the blade has you.
I assume you are talking about an intelligent items ego overriding the characters and becoming dominant for a day (or until a critical situation occurs). It follows the normal rules for "items against characters" and can become dominant at any level, however it requires a really low Will save so it is quite unlikely if it does happen. Usually your class features work with you instead of against and have the same alignment/goals so this should rarely happen.
An interesting interaction would be the blade attempting to become dominant when the magus is dominated by another spellcaster. A lawful good blade would definitely attempt to become dominant to prevent being used against fellow party members... An example of when failing a (low) will save is a good thing :)
How to prevent it? Get a better wisdom modifier, cloak of resistance, improve your will save through traits/feats and whatever you do, don't go against the blade.
An intelligent item CAN dominate someone that takes an action (or inaction, in some cases) that the item doesn't agree with.
Items against Characters
When an item has an Ego of its own, it has a will of its own. The item is absolutely true to its alignment. If the character who possesses the item is not true to that alignment's goals or the item's special purpose, personality conflict—item against character—results. Similarly, any item with an Ego score of 20 or higher always considers itself superior to any character, and a personality conflict results if the possessor does not always agree with the item.
When a personality conflict occurs, the possessor must make a Will saving throw (DC = item's Ego). If the possessor succeeds, she is dominant. If she fails, the item is dominant. Dominance lasts for 1 day or until a critical situation occurs (such as a major battle, a serious threat to either the item or the character, and so on). Should an item gain dominance, it resists the character's desires and demands concessions such as any of the following:
Removal of associates or items whose alignment or personality is distasteful to the item.
The character divesting herself of all other magic items or items of a certain type.
Obedience from the character so the item can direct where they go for its own purposes.
Immediate seeking out and slaying of creatures hateful to the item.
Magical protections and devices to safeguard the item from molestation when it is not in use.
That the character carry the item with her on all occasions.
That the character relinquish the item to a more suitable possessor due to alignment differences or conduct.
The save DC versus the item trying to control you is equal to the item's Ego, so having a high will save would be very useful, so having a high will modifier would be useful, as would having a high base will save based on your class levels. If you were a paladin, you'd gain the "Diving Grace" ability that allows you to add your Charisma modifier to your saving throws, and since the Paladin already has a high will save base, you'd get a character with a good chance to save versus the item's Ego DC. Other than that, you could be a halfling Pally and have the racial ability to add a +1 racial bonus to all saves as well.
Now, the Magus class also has a strong base will, so all you might want is to take a 2 level dip into paladin for the Divine Grace class feature for the charisma bonus to saves, or take some magic items that increase your will score such as the headband of inspired wisdom or the headband of mental superiority.
can a Black blade dominate a pc at higher later levels and how could that be negated.
Clear Spindle ioun stone, though alignment might be a weird issue and I'm not keen on how clear spindle works with anything that isn't evil or if there are protection from good variants or what have you.
I should add that usually the black blades motives are related to your own and it does share an alignment, so if it overcomes you it may not do anything bad.
If you were a paladin, you'd gain the "Diving Grace" ability
Paladin 2/Magus x would be pretty lame though. Two different casting stats, and you tend to dump charisma as a magus and intellect as a paladin.
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A Clear Spindle ioun stone do nothing against domination unless it is set in a wayfinder, and even if it is set in a wayfinder it work only against evil.
Protection From Evil: Does the "protection against possession and mental control" aspect work against non-evil controlling spells and effects?
No. The spell says "This second effect only functions against spells and effects created by evil creatures or objects." So if a chaotic neutral enemy casts charm person on you, protection from evil doesn't have any effect because neither the spell nor the caster is evil.
—Pathfinder Design Team, 03/01/13
Really, did someone tell them they overlooked the other 6 alignments?