It's true that 'civilians are in charge' but it would be an oversimplification to suggest that the military will just 'do what they are asked'.

Civilian leadership takes a few forms, there is a division between the powers of Executive and Congress. The military won't pursue anything long term without the backing of both.

There are a lot of legal thresholds, Congressional approval being just one of them.

There is institutional incumbency, and the military will push back extremely hard on things that it deems impossible, or excessively risky.

Populism etc. etc..

There are so many factors.

If they want to mount a risky 500 000 person invasion of Iran, they'll have to do a lot of 'convincing' and get a lot of buy in from stake holders. There is no chance that the Executive count mount that kind of operation without a lot of institutional buy in.