Those are not "exceptions", The great majority of Russian Muslims are from the north Caucasus, like the Circassian kids pictured above, or the Volga valley, they're not immigrants. These people have been living in these regions for over 1,000 years, they speak Russian, look up to Putin as their leader and are pretty well integrated into Russia.
en.wikipedia.org
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Russia had the opportunity for about 400 years from 1400 to 1800 forcefully convert the Muslim population. However, it would have severely hampered their expansion efforts, due to uprisings and even more internal issues and wars.
As you said, those Muslims have been there forever, they were simply conquered by white ethnic Russians.
Those calling for white Russians to separate are essentially just yearning for a smaller, weaker Russia which would ultimately be torn apart by civil wars, given that it would also be an excellent opportunity for more progressive minded Russians to demand a stronger orientation towards Liberal ideologies.
Would you take Haitians or Congolese over these Muslim Russian citizens?
African Orthodox Christians can't be compared to random Haitians or Congolese, even Serbs and Russians are in awe at Ethiopian Orthodoxy.
Furthermore, many conservative Russians would even take Africans over western Europeans. This is primarily due to the fact that the vast majority of Africans in Russia are students and Russian university graduates that speak Russian at the working proficiency level. Thus, Russians haven't been exposed to the bad ones, except when vacationing or via social media.
Secondly, there have been major wars and issues between western Europe and Russia. The current Ukraine NATO situation is yet another episode thereof. If Russia simply promoted transgenderism or gave up Orthodoxy, those issues would end instantly and western Europe would be on great terms with Russia.