From experience, the most common cause of Minecraft freezing on a heavily modded server is Java itself pausing to run garbage collection - it clears inactive data from memory to free up space. Normally on Minecraft this is so fast it doesn't freeze the game. On something like FTB though there's a lot of crap to clean up.
The obvious question is, if it is this for you, why is killing creepers enough to trigger it?
First off, try giving the game a little more RAM to work with. Maybe it's over-restricted.