Unlikely. If you look back at the last few issues, Karin was commenting about how Sasuke's chakra is dark, cold, and evil. These are some of the same things she said about the Fox's chakra inside Naruto.I was thinking when ol girl was comparing Naruto's dark charkra to the uchia's, Itachi's really. But then again she could be comparing Naruto's charkra to Killerbee's. Juat a thought.
Karin never once mentioned that Killer Bee's chakra was dark or evil. In fact, when we look at the interaction between Killer Bee and the 8-tailed Ox, we see that the Ox is much more helpful and friendly than the 9-tailed fox is. I don't think the 8-tails has evil chakra, but we know that the 9-tails does.
Itachi also wouldn't have had evil chakra. Itachi was secretly good: He saved his village, protected his brother, gave intelligence back to Konoha about Akatsuki, etc. This is all not to mention that Karin never really met Itachi in person, and would likely not know what his chakra was like.
I think Karin was definitely comparing the Fox's evil chakra, inside Naruto, to Sasuke's evil chakra.