Are the alkaloids even able to be dissolved in water?
What you can do is use a waterbath to avoid overheating it but it would be best to simply distill off most of the acetone. And then just letting the small rest evaporate if you wanna be really safe and avoid dry heat alltogether.
Also you really should look up if you maybe need to look into using drinking ethanol for the tincture if the active compounds of kratom dont dissolve in water.
Given that you already talked about having some distilling apparatus you can either buy high proof alcohol or concentrate it yourself.