Can someone pursue charges against a person making erroneous EO and IG accusations?

Can you? No.
Can a Commander with UCMJ authority pursue charges under Art 107 if a Soldier knowingly made false official statements with the intent to deceive? Yes.
It's a tricky situation, every complainant has whistleblower protection against reprisal.
However, the more unfounded complaints one individual has with IG and EO, the less likely whistleblower protection will help that individual.

Yes depending on the circumstances. However it is not a crime to make erroneous allegations they must also be knowingly false. So generally a complainant will be protected if they made the allegations in good faith, or if it can't be proven that they lied.

I've seen multiple investigations over questionable allegations in my unit. Usually when they cannot be resolved command just laterally transfers one or the other party to a different unit.

If it is proven that someone in the Command falsified statements there can be punishment given out to that individual. Happens all the time. The key is providing proof.