There's no need to house rule this — you just need to start enforcing its restrictions. Allow me to draw your attention to its area of effect:
4 square″ + 1″ square/level
(Aside, this is taken from PHB page 95, since the Illusionist version of the spell has different range and area of effect.)
These are table inches, which we could convert to feet/yards, but the following will be simpler if we just compare table inches directly with fireball's numbers.
A fireball has a radius of 2″. Let us ask then, “what level would an illusionist have to be to cast a phantasmal force large enough to contain a 2″ radius sphere?” Let's make a first-order approximation using the minimum number of 1″ squares necessary to create an area in which the image of the sphere could appear. The area of effect of fireball is three-dimensional, but the area of effect of phantasmal force is two-dimensional, which presents an odd issue. However, phantasmal force is described as being able to create images “within the boundaries”, so let's be as generous as the spell seems to be intended, and say that the vertical space it can create the illusion within is “good enough” for our purposes and we just need the footprint of the illusory fireball to fit inside the phantasmal force's area of effect.
We'll assume as a first-order approximation that each 1 square″ of area of effect can't be divided, so they have to be tiled as whole square table inches. Inscribing a 4-unit sphere's footprint (a circle) inside a pixelized shape requires a 4×4 square of squares, or 16 tiled squares.
So, as a first approximation, an illusionist needs to have 16 square table-inches of area of effect to play with to be able to make a phantasm of a full fireball. That requires being level 12 to pull off.
But maybe you think tiled squares aren't generous enough. Let's allow the table-inch squares of area of effect of the phantasmal force to be subdivided infinitesimally so that the area can be a cylinder that just barely contains the footprint of an illusory fireball and see where that gets us. (Some DMs might reject this move since the area of effect is given in squares and they may require a straight-edged area of effect, but some others might allow it with the reasoning that it's fine as long as the final area matches regardless of shape.)
A 2-unit-radius sphere has an area through its widest point of just over 12½ units, rounding up to 13 square″ required. So even being super-generous, it would still take an illusionist of level 9 to use phantasmal force to create an illusory fireball.
Clearly, creating illusions of fireballs with phantasmal force isn't something that your players should be doing at first level, or even 5th level when their magic-user friends are starting to throw real fireballs.
Conclusion: You don't need to house rule, just give the players a reality check
So, there you have it: you don't need to house rule this at all, you just need to pay proper attention to the relatively small area of effect, and break the news to your players that you've been accidentally letting them create a 9th-level illusionist's phantasmal forces before they were actually 9th level, and won't be doing that any longer.
If they are 9th- or 12th-level, then this isn't overpowered at all, because they have access to equally (or more) powerful effects already and cleverly using their resources like this should be letting them paste low-HD enemies by the truckload. So again, there simply isn't a problem if the area of effect is enforced.
Addendum: Don't overlook the audio limitation either
The above is all completely ignoring the impact of the stipulation that a phantasmal force is silent. Is a fireball silent? Not at all. An illusory fireball with no sound effects is not very convincing, and unlikely to fool even stupid opponents, even stupid opponents who have already been hit by a real fireball. In fact, having just experience a real one with all the sound and fury of real fire, they'd be more likely to notice that a silent one is not quite right.
You can use shadow conjuration, and you can use it to imitate sor/wiz conjuration spells even though you can't cast them the ordinary way. This makes it even more useful for a shaman than for a wizard.
Shadow conjuration does not say you need to know the spells being imitated. It does not say they need to be on your class spell list. It says they have to be "sorcerer or wizard" spells. It continues to refer to "sorcerer or wizard" spells even if you're not a sorcerer or wizard.
This isn't even a weird edge case about off-list spell access, because shadow conjuration is also natively on the bard list and on the darkness domain. It's clearly intended to allow vanilla bards and clerics to imitate wizard conjuration spells.
Best Answer
To the best of my knowledge, the issue is never directly addressed. The rules, on a quick scan, appear the same as in 3.5, where this issue has been debated some as well.
The long and short of the argument is this: the statement in shadow evocation et al. is that someone who knows that it is fake does not need to save. Nothing says he does not save or may not save, just that he doesn’t have to. This is taken to mean that this is optional, and effectively someone in this position has the option of automatically succeeding on his save the same way you typically have the option of failing any save. You may, according to this logic, choose not to automatically succeed, and then, since you are now attempting a saving throw, choose to automatically fail.
Strict-RAW, this seems most accurate, though it definitely takes a few steps to get there and it’s clearly not written out explicitly. Still, the language, whether it was intended to be or not, is precise: it waives a requirement to save, it does not add a requirement to not-save.
Whether or not you should rule this way in your game is more dubious. Shadow evocation et al. are rather useful, particularly for this feature. In 3.5, greater shadow evocation was typically used to cover the loss of contingency due to the banning of Evocation as a specialist wizard. In Pathfinder, this is less of an issue (since banning is no longer so absolute anyway). Most of the time, shadow evocation et al. are most useful when the drawbacks of using them (the Will save, the quasi-reality) don’t actually affect the functioning of the spell, which is precisely in this case: buffing. Ultimately, it becomes yet another powerful and flexible tool in the wizard’s toolbox, and he’s already got a ton of those. Shadow evocation et al. are’t the most powerful of them, but maybe it’s worthwhile to you to start paring down options where you can.