If this were a gigantea or a magnifica, I would recommend separating the clown from the anemone. But BTAs are pretty durable and should be able to withstand any stress from the clown. Also, I don't except the clown to immediately jump into the BTA. If it does happen quickly and the clown appears to be beating up the anemone (such as ramming the nem's mouth) then I would separate the two.
I'm sure you're aware that there have been several documented cases of BTAs causing Onyx clowns to lose their dark black coloration. I specifically removed my RBTA when my Onyx clowns were scheduled to arrive. They've darkened in color ever since I got them, and have a gigantea as their host.