I have good news on this matter. It seems all the problems where
caused by Android linker & implementation of System.load(path) which
calls JNI_OnLoad more than once, check
info on this matter.
I already created workarounds
which fixes the problem
and allows the apps to use Ministro again on Android 5.x+. We still
need to wait for 5.6.2 and 5.7.1 release to have the fix.
Big thanks to Roman Lebedev, who lead me to find the problem!