This is sort of a lot of work, but can be done a little more cleanly / less awkwardly by adding a second join against the participant table (do this only if the viewer is logged in):

LEFT JOIN %T v ON v.conpherencePHID = conpherence_thread.phid
  AND v.participantPHID = %s

Then always adding another WHERE clause:

(isRoom = 1 OR v.participantPHID IS NOT NULL)

(If the viewer is not logged in, this could just be isRoom = 1, since logged-out users can never see threads.)

That should be more resistant to mistakes than the status quo, while still giving the correct behavior (searching for both rooms and threads won't return only rooms where you are a participant).

As written, this also probably (possibly?) has the wrong behavior for logged out users, although I don't know if they can even reach any of this stuff (but they'll probably be able to via dashboards eventually, at the very least?).

This might create a sort of sketchy query plan; an alternate approach is to build a rooms query (if rooms are included) and a threads query (if threads are included) with their respective isRoom = 1 and v.participantPHID IS NOT NULL clauses, then use UNION ALL to merge them. That's more complicated and very likely not necessary, though. (Differential does this in some cases.)

This probably gets called before buildSavedQueryFromRequest() in at least some cases, I think. I'd maybe consider just returning Threads or Messages or something and dropping the isRooms property completely?