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Once "they've" run malware on your machine it's no longer your machine and nothing can be trusted. Wipe and re-install, then very carefully restore backups of data.
That is a general rule for malware that you do not know anything about.
However, the SearchProtect install bundled with µTorrent is only malware to the extent that it prevents you from changing your browser defaults. It is not believed to exhibit the other characteristics of malware. It is annoying, scammy, scummy, evil, etc. -- but it does not appear to compromise your system badly enough to require a reformat and clean install.
It's just one step beyond accidentally installing the Ask Toolbar with a new Java install. Yes, it is theoretically possible that it could've taken over your machine. But most likely not.
P.S. Take a look at the Wikipedia page for SearchProtect. Specifically, History and Talk. There's one high-up editor who's been stonewalling any attempt to add a Criticism section, on the basis that Wikipedia cannot link to user posts.
