I think this mission's probability should be extremely low if the player takes appropriate measures. What measures? well, for starters I suggest some sort or number of aliens vs. number of X-Com soldiers in the base (after all we can assume they're actually doing something between missions, including prisoner supervision and guard duty). Wounded soldiers and incoming soldiers don't count, but soldiers on away missions do, for the sake of simplicity.
The idea is, if you have 10 captured aliens and 30 active soldiers, the chance should be really slim, like 1:250 that it happens this month. If you have 10 aliens and 20 soldiers, let's make it 1:100. If it's 10 aliens vs. 10 soldiers, let's make it 1:50. However, it should never rise about 1:20, even with no soldiers in the base at all. (This is just an approximation, not a real function of course.) This can be further modified by alien type (Ethereals pose greater danger than Floaters) and soldier rank (experienced alien hunters are far better guards), but that could be overthinking things. And of course we can (and probably should) have other factors besides troop numbers, which I don't have ideas for yet.
As you can see, this would be an extremely rare mission, and actually unlikely to happen throughout your campaign. However, this is precisely the point: you make prisons to keep the prisoners inside, and prison escape is very unlikely. Still, it would be nice to feel the threat, and since it doesn't seem to be hard to implement code-wise, why not?
Oh, and one last question: where do they get weapons from?