Yeah, that really translates well.
In hoops half the guys play forward/center and half play guard... all using similar skill sets.
In football, not so much. A team typically has 2-4 QBs that could take a snap. The skill level typically drops off after the starter.
In hoops it's typical to take a player out for a few minutes to let him take a breather or provide some instruction,
In football that works for almost every position except for a very few. I'll let you guess which group a QB falls in.
In football, with a clear #1 QB, you normally* only take the QB out if it's a blowout (either way), the QB is hurt or the QB is simply having a bad game. You don't yank a QB for a series and then put him back in. If you need to talk to the QB, you do so between series.
Your suggestion of benching McNabb in the 1st/2nd quarter of several games, asking him to continue to be the starter and expecting the team to function as if everything's OK is just unrealistic (I'm being kind here).
* planned/scripted 1-set substitutions (Brohm at Louisville, Paulus at Syracuse) are the exception.