Hm. I've sometimes wondered how TNG would have progressed if it had held true to the intentions behind the scenes (e.g. saucer separation as a routine activity), but I don't think I've ever wondered how TNG would have progressed if the intentions behind the scenes had better aligned with what we actually got (e.g. would they have designed the saucer to be able to 'easily' separate if they didn't have the families onboard as part of the root concept?).
I think a better way to handle the concept would have been to have two separate ships, a large research vessel commanded by Picard and a more heavily armed and maneuverable defensive escort commanded by Riker. Maybe the research vessel could even have had a civilian crew and only the defense ship would've been Starfleet. I think that would've aligned better with the demilitarized approach to Trek that Roddenberry was going for. (One thing people tend to forget is that the original intent wasn't just that the ship had Starfleet officers' families aboard, but a large complement of civilian scientists and their families, whom the Starfleet personnel were there to support and defend. That's one more early concept that fell by the wayside, since for most of the series, the only civilian scientist we actually saw was Keiko.)
Maybe having two ships instead of one would've made the FX work more complicated, but
Battlestar Galactica managed to pull off a whole ragtag fugitive fleet 9 years earlier, pretty much the same way TNG handled the
Enterprise -- by building a sizeable library of stock shots in the pilot movie and recycling them going forward.
As for your suggestion, I'm not sure how it would've happened, since what you describe is pretty much just doing things the way TOS did, and Roddenberry's whole goal was to make TNG new and different in its approach. Also, the concept of saucer separation was always there in the background in TOS and TMP. "The Apple" referred to ditching the engineering section and using the saucer as a lifeboat, a concept also discussed in
The Making of Star Trek. Andrew Probert designed a prominent separation line on the neck of the TMP refit, and for a time there was a suggestion to include a saucer-separation action sequence at the climax of the film. So I think the idea of "Hey, let's use our bigger budget to finally show a saucer separation onscreen" was always going to be part of the development process. And that dovetailed with the idea of a more civilian approach, leading to the idea of routine saucer separation to protect the non-combatants.
Even if Bob Justman or Probert or the ILM people had come to Roddenberry and said "Nope, sorry, separating the saucer on a regular basis just won't be feasible," I'm not sure he would've been willing to abandon the idea of a civilian presence, and of the ship being oriented toward research and diplomacy instead of combat. That was very important to his thinking in that stage of his life.
Personally, I've always thought it would be refreshing to have a Trek series about civilian explorers rather than Starfleet all the time. The closest we ever got to that was
Picard season 1, but several of its civilian characters were ex-Starfleet. The
Prodigy cast were technically civilians in season 1, but they adopted the roles of Starfleet cadets, so I don't think it counts.