I have different sidurim from my family: one has a misheberach for Franz Jozef vemishpachto (by name), another for Nikolai Aleksandrovich vemishpachto. Clearly, it would not be possible to use both at the times when they were at war with each other! So, if we have those tefilos, it is probably OK to have tefilos for people who were freely elected by Yidden in EY.
Read the tefilos carefully. We are not asking for a brocha for anything they choose to do, we are asking Hashem to give them chochma (that they might be lacking).