Are you suggesting that suspicion of possibly maybe having put a trojan in someone else's files somewhere is grounds to make all one's efforts useless and poisons everything else you do?
Short answer: Yes. Downloading and running arbitrary binaries from the web inherently a quite dangerous thing do to, and I only feel comfortable taking such a risk with sites I trust. I no longer trust Sourceforge and there is very little they can promise me to make me start wanting to download from them again.