The Boltons have no real support in the North outside of themselves. Indeed, Roose notes that in explaining why they want the marriage; which only calls attention to the fact that Sansa doesn't gain anything by marrying them. With the rest of the North plus the Vale, she should be able to supplant the Boltons by force.
and how would that look like?
going secretly from house to house hoping one would rise with her against the boltons?
or go to war with the army of the vale behind her?
that war would only decimate both forces. and littlefinger certainly wants all of them intact.
besides, the crown backs the boltons. so they would have to fight the crown as well, I doubt they would just stand idle while a rogue vale army is taking back the north for a stark.
if they married and ramsay died it's a whole different matter, there won't be a war the crown would need to infere with. sansa is certainly not popular there but littlefinger can more likely do something about that. not about a stark openly attacking the warden of the north, that's a completely different situation.
marrying her and making her a bolton is obviously the easiest and fastest way to give her (and littlefinger) the north.