Maintaining Flap 30/40 has is not primarily about EGPWS unless you have some twisted priorities.
Its an option the manufacturer says you can use. It may well be appropriate close in or light and I'm guessing Boeing give you that option in order to avoid unecessary configuration changes and keep it simple. The EGPWS bit is a fringe benefit not the primary reason.
As the pilot you have to make the call. The better you know your aircraft, procedures and the more thought you have given to various scenarios then the better chance you will have of getting it right. If the scenario was indeed a large flock of birds on short final then in my view the correct call is to continue to land even if you then fly into those birds and suffer damage or an engine failure. This is because if you intiate a go around and then fly into them you could well loose both engines and be in an irrecoverable position and if you have already suffered strikes and have lost an engine you cannot gaurentee that your remaining engine is undamaged and will provide you with TOGA power so again you could put yourself in an irrecoverable position. The safest course is to accept the pain and land. If you are further out and are advised by ATC of bird activity on final then a go around would indeed be appropriate.
As I said earlier I admire the crew for keeping everyone alive and substantialy uninjured under great duress and pressure but I do wonder if the decision to initiate a go around (if indeed thats what happened) will be seen as an error albeit an understandable one influenced by many things including company culture.