Can someone be chaptered out after being found not guilty in a SHARP case?

Yes you can. You don't have to be found guilty to be separated from the Military. Being chaptered in an administrative action. It is not punitive. In paragraph 14-12c you can be separated for an event. The process is that the packet is reviewed by an O-5 and the O-6 is the final approval. You can add your statement but you are not given the opportunity of a hearing since it is administrative. In short, it's the Army's means of saying that they lost faith in you and they don't believe it is in the Army's best interest to keep you in. It just depends on what the O-5 and O-6 believe is best for the Army.

Either there's more to this or you need to go to JAG and the IG in that order, now.

Two points to make here:
First, not convicted / not found guilty is NOT the same thing as being innocent. It is entirely possible that the facts and evidence show that something happened but they did not feel they had enough to go to court and prove beyond a reasonable doubt. I am in no way trying to accuse you or say you did something. Just pointing out that from a Command perspective, they may still feel that where there is smoke there is fire.

Second, never pay attention to the rumor mill. Unless is is on paper, it isn't happening - at least not yet. I have seen more than one case where an entire chain of command was preparing a separation packet and everyone from the 1SG up to the BDE CDR was tracking the Soldier was on their way out the door, because there were very serious charges pending, only to have everything get tossed out once findings came back. With a serious allegation like sexual assault, the Command is going to want you gone as soon as possible once you are found to be guilty. Even before findings come back, they will be laying the groundwork (preparing paperwork, having you do as much separation stuff as possible, like mandatory portions of SFL-TAP, etc.) to make your exit as speedy as possible.
Now... once the findings come back clearing you, then you continue on your daily routine, and the paperwork gets tossed in the shred box. Just because they were preparing for separation doesn't mean you ARE being separated. And folks involved in the process may have not gotten the memo yet, and so the rumor mill still says you are being chapterred, even though the actual packet has been tossed out.

I am not saying EITHER of the above are definitively true - I am not in your unit, I am not involved in the process. Just pointing out things to consider.