I have always thought of the present tree view as more functional than pretty, so I personally wouldnt be nostalgic for it if it were replaced by an older more stable form. I went to your link, but unfortunately there wasnt any screenshot of what those older trees look like or how they function compared to the one we use, but if it comes down to a simple case of aesthetics, I personally think it is worth the sacrifice. But obviously that would be something everyone would have to agree on - because now something like a search feature would be redesigning the look of ompt - even if it has always been a function rather than form part of ompt.
As for the second idea of a separate window - that sounds great too, as long as we can preview the sounds, and drag them from the new window into sample or instrument places, that sounds just as useful as the original proposition.
It would be nice to have this ready for the next version of ompt, a bit of a "we have this great new feature in the update" thing, but yeah I think it would be far more important to keep ompt working properly and staying stable no matter what is thrown at it.
One final thought... I dont think the sample part of the search was freezing anything at all - and the original form of the search worked fine by greying out the soundfonts that didnt have results. It took longer to find the soundfont results over all, but you could still find them and go through them. As lovely and quick as it was to have ompt temporarily get rid of the non result soundfonts, just having the original version until you can come up with a method you are more confident in would be awesome.
In the end of the day, something like this search is something that will probably be refined and changed a lot over the years anyways, so I think this is something to experiment on.

just having the original version until you can come up with a method you are more confident in would be awesome.

No, that variant froze as well. Any variant that preserves how soundfonts are currently represented in the treeview will induce this sort of freeze.

It would be nice to have this ready for the next version of ompt

Unlikely.