Let's say I'm adjacent to an enemy. I spend a move action to stand up, and I wind up in the enemy's threatened area.
Now let's say an enemy's space overlaps mine and I'm prone. I spend a move action to stand up, and I still wind up in the enemy's threatened area.
There are corner cases where I'm prone with a free space to stand but multiple enemies still adjacent to me, but in that case the shift is really more of a drop of mercy in a flood of misfortune, wouldn't you say?
I think it's important to be consistent, and to avoid making exceptions just because it's nasty, without any in-game justification. I don' think it's reasonable to permit a shift because you happen to be under a threatening opponent - how could standing up be any
easier? Frankly, it's not a situation likely to occur frequently (since you cannot move into an occupied square, even if the enemy is prone, unless he's also helpless). Balance is important, and sometimes we turn a blind eye in its name - but this situation doesn't warrant that kind of leniency, IMHO.
For that matter, it's not particularly unbalancing so simply permit an OA from the creature above you when you stand up. In those cases where you're unconscious and an enemy stands atop you, it's not unbalanced to be disadvantaged. Any adventurer/monster with a say in the matter would have avoided being put into that situation, and someone can force his opponent to fall unconscious and then stand on him, he deserves to have the (literal) upper hand, right?
I don't think it's a balance issue to not allow shifts when a creature stands up from prone ever, and it is a consistency issue to allow it specifically in those situations where you're least likely to stand up easily. My vote would be to not allow such shifts therefore, and in any case to never penalize a player for
not having an enemy on top of his PC. A reasonable ruling could be to always allow one square of (provoking) movement as part of standing up, but that you can choose to forgo the movement and thereby avoid the OA(s).
On the other hand, in an actual game, I don't think this rule is important enough to have an argument about and I'd just play whatever the majority prefers.