It's misguided to assume that all tie-in fiction has to be "McFiction" just because it isn't original work. Sure, there has been a fair amount of tie-in fiction like that, but I think Trek Lit has proven over the past dozen years that it can be much more than that. It's a fallacy that creators have to lower their standards just because they're writing characters and worlds they didn't create themselves. I for one have always striven to approach my tie-in work with the same standards I'd bring to my original work, insofar as deadlines allow. After all, my tie-ins are potentially a promotion for my original work; I want people who read them to find my writing memorable enough that they'd seek out other fiction under my name. It would be self-defeating to approach them halfheartedly.
I'm really not sure that's what Joe meant, I think he may have been referring to the overall quality of some stories being, well shite and TCS not being shite.