All the SSR's were nominally organized on ethnic lines, even when the titular nationality became a minority (as in Kazakhstan). It was logical for Kaliningrad to become part of the RSFSR because its settlers, even if not ethnic Russian--which the majority would very likely be in any event--would be Russified (Ukrainians and Belarusians outside their own republics tended to be very Russified).
One other possibility that I mentioned once in soc.history.what-if:
***
In the past, we have discussed the possibility of Stalin giving the former
Konigsberg area (now the Kaliningrad oblast) to the Lithuanian SSR instead
of making it an "enclave" of the RSFSR. There is another possibility that I
don't think we have mentioned, though. It occurred to me while reading
Nicholas P. Vakar's *Belorussia: The Making of a Nation* (Harvard UP 1956).
Discussing the claims made by Belorussian nationalists in the West after
World War II, he notes that they rejected the boundaries of the Belorussian
SSR, and not only made territorial claims against all five Belorussian
neighbors--Russia, Ukraine, Lithuania, Latvia, and Poland--but that "even
East Prussia is included in the claims." Vakar quotes emigre publications as
arguing that East Prussia would be a "just compensation for the enormous
devastation which Belorussia suffered at the hands of the Germans" and would
give Belorussia "a sea outlet necessary for its economic development." (p.
279)
So suppose Stalin decides to follow this analysis? After all, he emphasized
the immense suffering Belorussia underwent at the hands of the German
occupiers as one reason for giving it a UN seat. "Comrades, the Belorussian
people are not greedy for territory--on the contrary, in the interests of
friendship with Poland, they have even given back areas like Bialystok which
were part of their republic in 1939-41. But is it not just for the
Belorussian workers and peasants to at least receive some of the territory
the German fascists used to attack them on June 22, 1941?" So Belorussia
gets the Kaliningrad oblast and a narrow corridor leading to it--perhaps in
the extreme northeast part of Poland (the Suwalki area--which some maps by
Belorussian nationalists claim as Belorussian territory anyway), perhaps in
the adjacent area of Lithuania. (After all, the USSR had restored Vilnius to
Lithuania, and by doing away with East Prussia had forever removed the German
threat to Klaipeda. In gratitude to Comrade Stalin for these great gifts,
the Supreme Soviet of the Lithuanian SSR is happy to grant his request to
cede a narrow strip of land to the Belorussian SSR for its great
contributions to the anti-fascist cause...)...