Now Whedon saying that he wants the SHIELD series to "stand apart from the Marvel movie universe" sounds to me like a Gotham Central show which would never mention the Batman.
I think that's a surprising way to interpret that particular phrase. He never said it wouldn't mention anything from the movies. He just meant that it needs to be its own thing -- part of the same universe, but with its own stories to tell rather than just being an appendage of the movies. Which, really, is the only way to do it. Look at any other spinoff series. Look at
Deep Space Nine or
Voyager -- they weren't constantly tying into
The Next Generation, but went off and told their own stories set in the same universe. They sometimes connected to some of the same continuity elements, like the Klingons or the Ferengi or the Maquis or Q or whatever, but they established themselves as their own independent entities with their own characters and story arcs. Conversely, when TNG went to movies, it avoided overt tie-ins to the Dominion War arc that was occurring on DS9 at the same time. After all, it was a separate entity with a target audience that might not watch the other productions set in the same universe -- and with a different set of creators who couldn't do their jobs if they were constantly having to follow someone else's lead.
For a Whedonverse example, look at
Angel. Although it did spin off two characters from
Buffy and did a fair number of crossovers while they were on the same network, it nonetheless set its own largely separate course, building its stories around new ideas rather than just continuing arcs from
Buffy. And once
Buffy moved to a different network, the two shows became even more independent of each other.
So really, Whedon isn't saying anything new here. His approach is the same that the approach to any spinoff would be. Whatever its connections, a spinoff is still a separate work, still its own production with its own staff, and it needs to strike its own course because that's the only practical way to do it. That doesn't mean it will
never reference its source material, but it does mean that, on the whole, it has to define its own independent direction.