They clearly aren't analogous. One was a completely made up conspiracy theory. The other has a bunch of evidence and various governmental agencies investigating it.
It's like saying that the "moon landing is a hoax" theory is analogous to the "Al-Qaida is responsible for 9/11" theory. There is clearly much more reason and valid evidence to believe one over the other.
Opinions are not all made equal. Some actually have facts, evidence, and rational arguments to back them up.
I understand the arguments being made, but I think it's best to look at the actual claim and the evidence used to support it. The problem in politics is that, very often, the people putting forth claims and/or rejecting said claims are already biased.