J, it's not made clear in the comic that she knows the SB is right next to the Collector General, BUT, she has got a small data cache that proves that the SB is working with the Collectors, and the reason as to why they wanted Shepard's body. It ties into Liara saying "and for whatever he's doing with the Collectors" in ME2, a motive that she doesn't state at the end of Redemption along with everything that happened to Shep, and that she's after the SB due to her love for him/her, but I digress.
I do think that there is a very distinct possibility that Liara is aware that the SB is aiding the Collectors and by proxy the Reapers. If that were so, then she is looking at the bigger picture with regards to the Reaper plot. If the most knowledgeable and influential entity in the galaxy is aiding the Reapers, then he needs to be stopped. Otherwise, the Reapers know everything about galactic civilization and then we're all screwed.