It doesn't resolve the "Brothers" situation at all, but perhaps the best compromise is that the saucer has a "warp sustainer" engine similar to how photon torpedoes work. Fire at warp and they stay at warp, but they can't get to warp by themselves.
Alas, that contradicts "Arsenal of Freedom" where the saucer was launched at impulse for an interstellar journey. LaForge had no excuse not
to give an initial warp boost to the saucer if such a boost were the only way for the saucer to enjoy a "Farpoint" type spell of warp speed. If the saucer could accelerate to warp all on its own, though, the maneuver makes sense.
(FWIW, the separation in "Farpoint" also takes place with a sublight
starfield in the background - perhaps suggesting that warp separation is flat out impossible and the heroes in fact achieved dead-stop-plus-separation at the end of a high warp run...)
In "Brothers", the heroes specifically struggled to force Data out of warp. Probably they could engineer a situation where this would happen to the saucer despite it having the ability to independently maintain or reach warp. Say, Data would be hard pressed to manually activate any systems (he couldn't leave the bridge, he could merely press buttons and tell the computer to do things within its powers), and the saucer warp drive might be inactive in combined flight mode and require the cooperation of dozens of pairs of hands to get online.
The discrepancy with "Encounter at Farpoint" has a real-world explanation: based on on-screen evidence during the first several episodes of TNG, the VFX guys and producers clearly wanted TNG's warp effect to mimic TOS's. The warp streak we all know so well wasn't introduced until a few episodes into the series. The Enterprise
was clearly meant to be at warp during the separation sequence in "Encounter." Based on this, it is difficult to conclude that the Enterprise
was at impulse in "The Arsenal of Freedom."
Second, and I can't remember where I've read this, but I believe the saucer was meant to have a "warp coasting" ability when the separation sequence was first conceived. This would allow the ship to stay in warp for a time before gently reverting to sublight and would reconile the conflicting information presented in "Encounter," "Arsenal," and "Brothers." Picard may have intended that the saucer fall gently out of warp after coasting for a while, not for the saucer to be instantly wrenched from warp. And, this would have allowed the saucer to reach Deneb and flee Minos in those respective episodes.