語源由来辞典 lists theories that they might be connected for the very same reason you mentioned, among others.
The way I understand it, it is generally believed that 腐る, along with くそ, stems from 腐る, but that is not proven (and there are other conflicting theories, such as 腐る stemming from 糞荒【くさあるる】, whose reading I can't quite explain).
Apart from that, I've been able to retrieve two related citations from the 岩波古語辞典, from two different sources.
The first one is for 腐り, from a Yahoo! question.
The second one is for 臭し (classical form of 臭い), which can be found here.
As you can see, both entries cross-reference each other.
So, it seems like the 腐る・臭い connection is definitely the most agreed upon theory, although there does not seem to be a definite proof. There definitely seems to be some kind of connection between (at least two of) くそ, くさい and くさる, though, although we can't know for sure how exactly it's laid out.