The fact that he was acquitted means he would not be a good example of deciding whether or not we were at war since he was, well, acquitted. There appear to have been a few treason convictions for the early rebellions, and one could argue that Mary Surratt could not commit treason if we never considered those states in Rebellion to be another country (though hers is complicated by being a military tribunal).
Despite the debate over wording, treason convictions, or even charges, are really rare with the last ones having happened during WWII. There are probably many other charges that would be easier to convict than treason outside of a declared war. While I feel Flynn may well be over the line of treason if it can be proved that he did Putin's bidding here, feelings do not convict a person in a court of law. Why indict somebody on the high bar of treason when you can have a much higher chance of conviction with the same severity of the sentence if you try them on a different (lesser) charge?
IANAL but IMHO, I don't think courts exist to assuage our feelings about a particular matter. The job of the prosecutor is to convince a diverse jury of Americans that the evidence shows, beyond a reasonable doubt, the accused committed the offense for which they are charged. It has to be proven to people who are very likely not like me and don't think like me.