Debian packages are signed. It is hard to make software distribution completely secure. But, one could imagine creating pretty strong guarantees. Imagine that you have N completely different parties/machines (isolated, on different infrastructure, different user accounts).
- (N-1) machines build a new Debian package.
- The (N-1) results are fetched by the fourth party.
- The Nth party checks whether the build results are identical.
- The Nth party signs the result with GPG on a machine that is not connected.
- The signed package is distributed.
An attacker would need to compromise either: (1) N-1 build machines; (2) the offline machine used for signing packages; or (3) the upstream source.
I consider (3) to be the most serious thread. But in this scenario, only the distribution packagers need to inspect the source changes. In the common scenario where you download from a vendor (e.g. the Transmission or CCleaner website), every user has to inspect a binary blob.
Another possibility would be to have strong sandboxing for applications. An application could still participate in DDoS attacks, etc. But it would at least not encrypt/destroy your data.
tl;dr: reproducible builds are an extremely important development and Debian (and other distributions participating in this initiative) should be commended for their work!