Not a solution to the problem as it doesn't work with items and is kinda difficult to do but it might help at some point.
You can remove any mobs of a specific type by running this command:
java -cp replaymod-1.0.5.jar de.johni0702.replaystudio.launcher.Launcher -c '(b)(a>remove_mobs,{Types:[CREEPER]}>b)' input.mcpr result.mcpr
This assumes you're in the same directory as your replaymod-1.0.5.jar, the input file is called "input.mcpr" and the resulting replay without those mobs will be "result.mcpr" (both in same directory).
You can replace CREEPER
with any of those. You may also remove multiple in one run by concatenating them via ,
(no spaces).
Edit: This is the command. The forum seems to have messed up some parts of it.