Could a hacker replace Bitcoin QT in some Linux repository and steal Bitcoins? Bitcoin QT, being a Linux application, is updated regularly when the application in the repository is being updated (For example, apt-get upgrade on Debian).

Theoretically, if a hacker could get into some Linux repository, he could replace the application with a malicious one that steals both the private key and the wallet file and send it to a remote server (effectively stealing all the Bitcoins from most the users).
If possible, even through social engineering, the incentive for such hack is enormous.

How likely/unlikely that to happen?
You know you don't have to trust the repo. The developers of Bitcoin-QT actually recommend using their binaries rather than the distro's. So you can just keep up to date with those. Official binaries are signed with a Bitcoin-QT developer's PGP keys.