I've never had that issue. The macro always cancels her auto-embrace for me. However, I don't spam it (spamming messes with the macro even with macro lock). I press once and she starts what I tell her to within 1 second).
Of course it'll be nice to not have to worry about it at all anymore (and it'll be nice for summoner, who couldn't effectively use the macro method because changing steady/guard actually affects how their pets behave).
All in all a good change, and the FU changes sound more interesting. I already use FU quite a bit but sometimes I wait because I know I have a pet skill I'm going to be using. If she's able to interrupt FU in order to use her own skills, that's a huge improvement.