LCN, you point out an anomaly: Connie says, "Michael wants to take him to Reno now [emphasis added]. But Michael's still in the boathouse when the shot rings out, so he obviously didn't take Anthony to Reno.
IMO, FFC had Michael in the boathouse, instead of on his way to Reno, as a dramatic device--so the current part of GFII could close with us witnessing Michael's ultimate decline into crime: hearing the sound of his brother being killed on his order. Realistically, Connie probably would have noticed that Michael didn't take Anthony to Reno after all. That would certainly have contributed to her (eventual) realization that Michael had Fredo killed (I'm one of those who believes she did). But it doesn't make her an active participant in Fredo's demise. Remember: Connie was the one who pleaded with Michael to forgive Fredo.

Now, there's a possible clue to Michael's character here. In GF, Michael cynically has Carlo murdered on the day he stood godfather to Carlo and Connie's son. How did he reconcile that? In the novel, Tom points out to Kay that it wasn't Michael's idea to stand godfather to the infant: it was Connie's idea. Projecting that subtext into GFII: it wasn't his idea to forgive Fredo--it was Connie's idea. Perhaps she realized that after Fredo disappeared and simply blocked out the horrible thought.