It all comes down to whether this procedure makes a significant difference in his performance. If Javy comes to ST and hits, and then starts the season and is doing reasonable damage at the plate, he'll fit in well enough. If he doesn't, then yeah - you've got a problem. The worst thing that can happen is that for whatever the reason, they can't get a good read what his performance projects to be so things drag out into the early season and becomes a distraction.
If the performance isn't there, I don't see what they can do other than DFA him. Trade would seem impossible. You just hope the DFA decision if necessary, can come sooner rather than later.