I would make the case the "big" diffs are a problem. Unless there's a really good reason (and bad dependency management is not a good reason) then commits should be smaller and more logically related.
This is a merge commit, which means the diff is going to include all the changes on the branch being merged. Even if all the individual commits are small, a merge diff can still be very large.
While I agree that a big diff isn't a good idea, I disagree with the notion that one should develop in such a way that makes Github (or whatever VCS you're using) work right.
I don't think working within the capabilities of the VCS you're using should ever be a priority for a software development effort; rather I think the VCS's priority should be to allow for their use within most contexts of software development. (the other way around)
" This change deletes the C implementations of the Go compiler and assembler from the master branch." is logically related as it could be. Everybody has a different interpretation of it, I guess.