The only relationship I recall Stewie really sabotaging was with Jillian. But personally I think the final episode (should it ever happen) will have those two getting together.
Brian is the one who sabotages his own relationships. He's too self centered to realize the needs and wants of others and rarely puts aside his own beliefs to help them out.
Stewie just happens to be the guy who plays off his flaws in the typical flamboyant male style. Although he was quite an annoyance when he moved into Brian's apartment.
It makes sense if one ignores the fact that Brian has no romantic interest in Stewie whatsoever. Yeah, there's been jokes of Stewie liking Brian, but never the other way around.