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.
LaForge ordered full stop prior to separation, 28 seconds out of Minos and ordered Warp 5 on the stardrive after separation. By all accounts, the ship was not at warp during separation in Arsenal.
Additionally, there's no reason to assume that Starbase 103 was outside of sublight range for the saucer. LaForge was pretty specific as to where and when he wanted the ship stopped during separation prior to ordering Logan to take the saucer there.