I think that Hunter might have joined, but only at first. And you're right, there's no way he would have agreed on the matter of Coulson. He would have tried to talk Bobby out of it, to make her listen to her own doubts on the subject, rather than the clown committee, but I doubt it would have worked.
In the end, Bobbi would have remained loyal to Gonzales and "real Shield" (God, I
hate
that name!), while, when push came to shove, Hunter would have stood by Coulson and Skye and Fitzsimmons and the others. So I don't think it would have changed much although at least he wouldn't have felt so betrayed.
sigh Damn, I miss the guy
"We're a team, Garrus. There's no Shepard without Vakarian."