^Yeah VOY messed up the Q as much as they did the Borg, in some ways.
Why?
Because it stuck with the premise 'the more advanced tech you have at your disposal, you and your culture will appear as 'divine' to others?
Or was it because Voyager crew used Q weapons to fight in the civil war?
It was established that Q can be injured and even killed with the proper technology (Q tech in this instance).
The Q are simply more advanced technologically, and possibly mentally in terms of portraying abilities (although technology was used on numerous occasions to create an illusion that someone has certain abilities, when in fact, they didn't).
Voyager episode 'Death Wish' for example had Quinn tell Tuvok the following:
'We may appear to be omnipotent to you, but in reality, we're not'.
He also told him that to numerous races who are on a more primitive level of technological development, Voyager and it's crew would appear 'god-like' and that it's no different with the Q.
Why is there a need for some humans to glorify anything more powerful than them (or things they don't understand) as 'gods', or in any religious sense whatsoever?
That's such a primitive way of thinking that it's not even funny ... especially in this day and age.
I agree that there are numerous things we cannot explain, but resorting to religion is equivalent to saying: I don't want to understand it because it requires too much thinking.
Q and the Wormhole Aliens ... well, in the Wormhole Aliens defense, they did have an actual Wormhole ... an object that interacted with linear time and was accessible to corporeal entities.
Thus, the Feds had an opportunity and time to study how it works, although certain aspects of it's function will still take time to decipher as their own knowledge of the galaxy and universe grows.
The Q on the other hand don't really have their 'toys' dispersed throughout the Milky Way (at least from what we know), and as a result, the Feds really had no way of analyzing, much less understand on makes the Q tick.
Power-wise, for all we know, the Q and Wormhole aliens are evenly matched.
We just have too little data to go on.