Okay, I'll give you the caring for friends/your own people trumps the far away foreigner, but what is the danger to Londo? What is Vir's concern? That Londo will lose the respect of Lord Refa? That Londo won't eventually become Emperor? At this point we don't know how far these people will go (poor Prime Minister Malachi!) and I don't really think Vir was concerned about Londo's safety. His reputation and his career maybe, but then we're back to not very good reasons.
Did Vir completely grasp what was going on? Londo doesn't 'get' what happens to Malachi, at least not immediately, so Vir probably didn't either. Maybe it's a function of his goodness, his innocence, that he doesn't take it seriously enough.
And there is still the issue of whether it would have helped. Who does he tell? What does he say? Perhaps he's trapped in silence.
Later Vir seems more concerned with Londo's soul (if that isn't too grandiose a statement). He wants Londo to make good decisions and regret his prior bad decisions for purposes of his own redemption. Vir eventually cuts himself loose from Londo, but without ever throwing him over completely--he always cares, does Vir.