Can I be counseled and forced to run every duty day for running a 17:45 two mile?

Yes, 21min is the standard for the ACFT, after five other events.
If you are just warming up and running, and reasonably fit and under 35, then 16min for two miles is a reasonable and obtainable time.

Running every day won't "destroy your knees", and I assume you are really talking about five days a week.
Six months after I tore my ACL, I started running six days a week and maintained that for 10 years with no overuse injuries.
There are many runners who run seven days a week most of their adult lives with no issues, not just pros, but many more who are just people who like to run.
But you do have to vary the distance and pace.
Doing the same run every day will not result in improvement and will increase the risk of overuse injury.

If you and your partners were "breathless" after that last run, well, that's what running is like when you put effort into it. If you can easily carry on a conversation during a "run", then you aren't running, you're shuffling.

I appreciate that you want to focus your efforts on "performance and knowledge of your job", but the Army would prefer that its people put their best effort into everything they're asked to do.
And since nothing else is going on during PT, might as well put that best effort into PT while you're there.

Everyone said what I would have said but I did want to point out that the ACFT is not the test of record. Currently we have no test of record. We need to be ready for anything. With all the push back and false starts with the ACFT. It could always get changed. And if suddenly we are required to take an APFT. 17-19 minutes won’t cut it for most.

A counseling statement is a record of a conversation. So, yes, you can be counseled... For just about anything, really. Provided that what your statement says reflects what the conversation said.

For some reason, the Counseling statement is STILL viewed as a negative thing. It is not. If what is being said (and documented) is accurate, and you feel that it reflects negatively, then the onus is on you to change yourself and correct the negative aspects. If what is being said (and documented) is *not* accurate, there is a spot to write "your side of the story." Being counseled is not a negative event - even being "negatively counseled." It identifies areas for growth - which is a good thing.

As for making you do PT, well.... As long as it is on "Army time," if that is what your NCOs feel is the best thing for you to be doing then that is what you do. It is up to the NCOs to train you in ALL aspects of your job - and physical fitness is part of your job. If it gets into you having to "stay after," then it becomes punitive. And they cannot punish you unless you have failed to meet an actual standard, which is not the case here. But, a word to the wise: They CAN strongly encourage you to work out on "your time," to include working out with them in organized PT "after hours." You are not required to participate, but expect refusal to be documented. Not as a punitive action, but in case you DO fail an eventual ACFT, they have documented the efforts they have taken to try to help you, which you refused.

I will grant you that there are plenty of NCOs in the Army that are just dicks. They get power and want to (ab)use it. But, in my experience, these are FAR outnumbered by NCOs who legitimately want to help every Soldier under them - and many who are not. I strongly encourage you to take a step back and lose the defensive attitude. Take a look and see if maybe, JUST MAYBE, those NCOs are actually trying to square you away. They might not be. They might just be dicks. But try looking at the situation and assuming they are not, and see how it looks then.