There are two issues you have to worry about. Consider the probability of each happening, and then the ways in which you can decrease those probabilities.
1. You hit your target, bullet keeps on moving.
This rarely happens, even with FMJ, though 9mm FMJ has the highest probability of doing so. JHP's whether they expand or not, are not very likely to exit the body, unless we're talking about arm shots, or something. This is however, next to impossible in a pre-frag design. The potential problem, however is that this pre-frag bullet will fail to stop the target. Again, the odds of an attack not being stopped by a decent hit are slim, as most attackers/intruders are not very determined, there are some that are, and being prepared for them is wise.
2. You MISS your target, the bullet keeps on moving.
I believe, from what I know about pre-frags and what I've read about them, that they will offer the least threat to bystanders in this instance. FMJ, and JHP's will both penetrate to nearly the same distance through dry material. The Federal EFMJ here offers an advantage. It expands in dry material (like plywood, sheetrock), and SHOULD (though I've not seen the tests) penetrate less than a FMJ/JHP, though more than a pre-frag. The EFMJ's perform in people about as well as other JHPs.
Best bet: shotgun.
For a handgun I'd tend to recommend the EFMJ over the pre-frags in this situation, but you might be more worried about stray bullets than I am.
In either case, target practice helps to reduce the threat of wounding innocents more than bullet design.
-Morgan