Crimson Caravans and Silver Rush are intrinsically mercenary operations. The former may nominally be NCR, but they don't really value anything more than money. So it really shouldn't matter whether you're Legion or NCR really.
I tend to go pacifistic since the ending does make it clear that screws get put down on businesses like Crimson Caravan and the VanGraff family starts feeling the pinch. If you kill Alice McLafferty and the local Van Graff clan, then Rose starts attacking caravans which forces trading companies out of the Mojave. This is inherently bad if you're going for Independent, House or NCR; and very probably Legion victory. It is never a bad thing to trade. Rose's storyline is pretty cut-and-dry about impulse control, it's not about good or evil or what cause you serve. It's about having power and not using it.
Basically my analysis is very consequentialist. I lean to Independence and such a cause is still best served if the caravans still do business as usual, even if the NCR has withdrawn from the region. Your immediate problems is that there is no central government and you still want outlaying settlements to prosper. Trade improves that situation immensely.
I take a very Followers of the Apocalypse view of things. First, do no harm. Extant harm is a fact of life. But it is little good to propose a cure that's worse than the disease. Rule with a light touch.