I think it would be a pretty cool twist for Gomez to be working with a cartel. Imagine Hank finds out his two closest friends in the show have been working against the DEA all along.
I don't think the notion itself is
that terrible, but people would absolutely hate it.
There are plenty of legitimate reasons it would be a bad idea for the show itself, but I think we're now programmed to hate moles. God bless "24", but they destroyed moles forever.
Breaking Bad is supposed to be above that sort of thing.
I don't see it, but I think Gilligan could pull it off if he was so inclined. More so, I'm confident he's just smart enough not to go down that road.
Aside from the general hatred of moles, people would be pissed because BB is so focused right now (as it's always been). We've seen the consequences and destruction coming for so long now, and it's almost here. Throwing the mole wrench in the middle of this would just be a disaster.