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Yes, they can chapter you on that basis. First, you were not found innocent. You were found "not guilty." The distinction is a legal one. Being proved innocent means having facts that establish you did not commit the crime. Instead, you were found "not guilty" which means not enough facts established your guilt for that civilian court. It's an important distinction here.
Second, the military is not bound by the determinations of a civilian court. They are two separate jurisdictions, each with the independent power to make their own decisions. The military can use the underlying facts and submit a separation based on their own view of the facts. Furthermore, we are dealing with different burdens of proof here. In a criminal case, the evidence has to be "beyond a reasonable doubt" a very high standard. However, to chapter someone, you only have to meet a "preponderance of the evidence" because it is not a criminal action, but an administrative action. That is a much lower standard. Facts that can't meet a criminal law standard may be sufficient though to meet the lower administrative discharge standard.
Regrettably, people are separated all the time for making just one mistake. This is even more true now, given the shrinking military.
You'll have the opportunity to submit a rebuttal and you really should, but it should be a plea to remain in the service and evidence showing your rehabilitation. They can choose to suspend the separation and just hold it over you, like probation, for 6 months to a year. This is an option you can reasonably request, but it is going to be based on the discretion of your command.
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