The red gate isn't just open upon the beginning of the scene, Lucca still has to open it...
Lavos was 1) being drained of his energy via the Zealians 2) a lil drained after (or saving up for, I forget which occurs first) completely ufcking the Zeal continent and 3) isn't completely full of power as it is for it's eventual birth in 1999. Plus, I don't see any of the Gurus as being a threat to Lavos after they're gated...Belthasar goes insane, Gaspar really can't go anywhere, and Melchior...well, what's he gonna do in 1000AD?
You could also see Magus' Castle as being a partial accident I suppose...Plus, I think it's possible that Magus was gated in the original timeline, I don't think there's enough, exactly, stating that the gate was purely the fault of Crono & Co. All we get is Magus blaming them during the accident...and he's quick to blame anyone for anything really...I suppose I could also see this gate as being an Entity gate...but I don't see why the Entity would send Magus anywhere, much less why Magus would go somewhere different...I'm ready to blame it on an accident...
I'm also under the assumption that the Entity doesn't have very much power (being killed by Lavos can do that to a...thing...). I see the regular gates as being made pretty much all at once as a last, ditch effort and the red gate, which only lasts for a moment, shows how underpowered the Entity is at that point, I believe...Rather than making a complete gate, it simply makes a temporary one...