Should/will the Rebel Captive crew upgrade effect the new Scum and Villainy faction?

No reason it wouldn't. It will effect imperial ships in imp vs imp match ups.

oh that makes sense, thx

If you need a reason for it, one assumes that the Rebel Captive in question is of sufficiently high value that everyone would like to get their hands on it, and would thus be reluctant to shoot at it and risk blowing it up.

For the Rebels, it's probably one of their commanders, who they'd much prefer to rescue.

For the Imperials, it's a high-value intelligence source, who they'd much prefer to question.

For the Scum, it's a high-value target, period. You capture those and hold them hostage, or turn them in for whatever bounties they may fulfill. In a faction driven by credits, you'd expect them to feel a bit stressed after discovering that the shuttle they were unloading on had a bounty worth 50,000 credits aboard. That's a lot of money they're at risk of losing.