Cordelia is the only person who could have had any real influence on Wesley's decision. He could have trusted Cordy to take care of the baby while he dug deeper into whether they were dealing with Angel or Angelus.
You do have a definite point here, but, if there were any chance that they were dealing the possibility of either Angel or Angelus threatening Connor, it's quite likely that Cordy taking care of the baby while Wes did more research on the matter, it would still have involved someone, in this scenario, Cordy, taking Connor away somewhere where he would be protected from his father, preferably with someone there who would be able to defend the baby if things actually did turn out for the worst, which could have been a fantastic opportunity for a Buffy/Angel crossover, especially if Buffy wound up recruiting another vampire to help her protect the baby. (See there, Thetopher, just for you, because you were expecting it, I shoehorned Spike into the story line)
Anyhow, whoever did it, and however long it would have had to take to disprove the false prophecy, the only safe option would have been to take Connor somewhere where he would be safe during that time, and I still believe that Angel would resist that action, no matter who proposed it. Best bet would still be Wes taking Connor, in this case, to Sunnydale, hoping for help from Giles with the research, and Cordy staying in LA to explain things to Angel, but, for my fantasy crossover to take place, she would have to be unsuccessful.