Eh, I think you are messing up the timeline a little. Marines arrive and the negotiations happen, Lucci starts sending info, the escape plan is made and for that Franky, Luffy, Lilith and Bonney go to transport Sunny. Kizaru arrives and starts fighting Sentomaru, at this time Luffy and co are already away from the rest of the group and Luffy senses Kizaru. Kizaru beats Sentomaru, gives new orders to Pacifistas and then bypasses the laser barrier, at this time Luffy and his group are transporting Sunny. This is when Lucci makes his move and is then thrown outside by Zoro after which/simultaneously Luffy and Kizaru engage.
If Lucci was just waiting for Luffy to leave then there was quite a big window of opportunity. He already knew that Kizaru had arrived and Luffy was already away for the transport and then Kizaru fought Sentomaru too and after that when Kizaru bypasses the barrier does Lucci make his move but this is before Luffy engages in battle with Kizaru.
What I am trying to say is that Lucci not striking earlier was more due to not having Kizaru as backup rather than Luffy not being there. We already know that even when Luffy was present Lucci was still prioritizing targets and not stopping in his attempts to kill the target (Sentomaru).