Pretty standard Trek fare: energy beings taking people over's been done at least once a series.
I also thought Archer pretty close minded right off the bat, but then again -- just about every alien they run into has ultimately been hostile...
Locking people in their rooms while 'possessed': makes sense to me. Don't want them wandering about doing who knows what...especially as they aren't asking permission to do these crossings. The first one or two, you take their workd for things; when it starts happening ship-wide...
This Starfleet is still military-oriented. The CO of a ship is going to react to avoid trouble before it happens, when he can.
"War is an ugly thing but not the ugliest of things; the decayed and degraded state of moral and patriotic feelings which thinks that nothing is worth war is much worse. A man who has nothing for which he is willing to fight, nothing which is more important than his own personal safety, is a miserable creature and has no chance of being free unless made and kept so by the exertions of better men than himself."
John Stuart Mill