This all seems a bit 'mountains and molehills' to me.
Manys a time I've lined up the commercial and said to the transit "319/737 shortly departing R/WXX route east/west of the XX threshold" or "pass behind the departing 319/737 R/WXX"
Ergo the commercial gets what they want and the transit has to turn a few degrees left or right but there is no major inconvenience to anyone.
I know GA pilots don't like it very much but there is one inescapable fact that these days which runs most ATC units (certainly mine and Chilli Monster's are good examples). We are first and foremost employed by (or contracted by) the Airport Authority to shift traffic into and out of their airfield. Everything else is becoming more and more secondary but that is not to say that we will go out of our way to be obstructive to GA traffic. After all, we don't 'own' the airspace around us, we merely manage little parts of it on behalf of the government (and their various bodies).
Take the controlled airspace we were granted a year ago at Brizzel. We have to keep records of all transits through our zone and we mark them down as 1) the pilot was allowed to continue as he requested, 2) the pilot's requested route was modified and what he was given and 3) the pilots CAS transit was refused. For the last two, we also have to give a reason why the pilot did not get what he asked for. It's a pain in the a**e, but we do it because we have to prove that we have not closed off the airspace we were granted control of to other traffic.