Yes, I wouldn't want a Trek show to depend on selling toys, either. That would almost certainly generate episodes that I would not enjoy watching.
The only cartoons that do that are those based on card games and interactive toys (Pokémon
, Tenkai Knights
, etc.), and even then they're not that different from shows which just introduce new characters and story arcs along the course of their run.
A new Star Trek animated series could be (if not likely be) more along the lines of the original as far as its writing is concerned, but with a toyline and other product lines attached to maximize its merchandising potential. In that sense, it'd be totally no different from the live-action shows as they all had toylines.