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Typically, you do the quests for each side up until they ask you to destroy the other's ship. That's usually when you would rescue the prisoners and get the alliance. So yes, you should go to Bayjin first and take care of Glumph. Especially as he has to join the party, and you wouldn't have room for him if you rescue the Templar prisoners first.
As Scatter said, entering Ascension Peak with no or only one doodad prevents the Rapax from blocking the place off. However, if you've already been there with two or more, the landslide has happened and you can't get there again from Bela's side; you'll have to use the Rapax portal.
There is no absolute need to kill the Rapax king or rescue the queen. All that matters is getting the two prisoners out there in one piece. The usual place to set a portal is by Z'Ant. Open the two cages, then talk/recruit the prisoners, and portal away before the Rapax can react.
Nightowl2
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