Capturing human player ships in D2 caused a CTD (crash to desktop). The bug probably hasn't been fixed in D3 so it was easier to disable the option. In D2, I got around this bug by ending the mission even if the human player had other ships to escape to (obviously transferring to another ship is not available in SFC3).
I'll have a play later this year to try and find a way around the problem. Look out for my 'Mission Fun Pack', it'll be free to download and will be available for both SFC2:EAW and SFC3. All missions will be playable in both single-player campaigns and metaverse campaigns (online). Some surprises will be in store, these include random team starting positions, random asteroid fields (except in multiplayer), random 'visual candy' such as planets etc, AI interventions, mission balancing, cowardly AI captains and a few surprises !