First of all, Sotomayor is of Puerto Rican ancestry; all Puerto Ricans are U.S. citizens.
Second, do you think that Justice Thomas should recuse himself from all civil rights cases because they involve "his people"?
The left does not see it the way that we see it. To the left, identity politics trump other considerations. Puerto Rican is still considered Hispanic so she has solidarity with the illegals. If you doubt me, please look at her political activism and writings. She considers herself part of the oppressed minority, a laughable assertion given the privileges that have been bestowed upon her.
The left would prefer that Clarence Thomas recuse himself from all cases involving race. Clarence Thomas does not seem to play the identity politics game so he is reviled in the African American community.