Lots of good points.
1. Its clear starfleet lacks military knowledge. A private fresh out of boot today could critique all the tactical errors in startrek.
2. Good call on the rights of sentient holograms. but who says they have to be sentient? depending on the complexity of their subroutines they can be sentient, or they can be simple machines. After all, even humans are machines. Complex ones. In VOY - flesh and blood belanna thought just as I did. "you liberated MINDLESS machines". And she was correct. it begged the question, even the holograms use consoles, ships, and machines. Their very own logic could be used against them. What if the ship had a computer core that was itself capable of sentience ...would the holograms not be guilty of using it as a tool? They use machines all the time as well. They also take them for granted because they do not recognize them as beings..until it begins to think for itself, then they fight for their own ideals. Or in their own logic they said "it doesnt MATTER they are children of LIGHT and I will LIBERATE THEM". This would be akin to us saying a virus deserves the same respect. After all...we could always genetically engineer it to grow into a multicellular sentient life form right? no one has a right to kill a virus .....
A hologram need only be as simple as todays drones and autonomous weapons. They need only identify friend or foe, they only need to rove the ship and only need to discharge weapons on foes. This is doable with todays technology using non photonic machines, and it hardly involves sentience.
To those questioning them being reprogrammed ....or some other stuff. really ....think a boarding situation through. I mean seriously ...tactically ..beginning to end. And if you think our military is even NOW ..near as "inept" as starfleet at intelligence leaks ..and tech problems ..think again. Encryption is a big deal and there are actually procedures and contingencies in place. Hundereds of times in startrek I find myself going "WAIT .....you know what could happen right??? why isnt your crew standing by to execute contingencies ...why do you even NEED to send a command??"
Startrek is mostly Plot moving ... very little actual science and very little military aptitude. it would be easiest to refute on a case by case basis.
My fav eps are always the philosophy ones
. Inner light, who watches the watchers, all good things, the host! very good one Even the borg eps. Even though ..The borg would be easy to beat o.O