Just before commencing the roll, we noticed many birds flying just at some height above the center of the runway.
I gotta say I completely missed that part.
I agree with freqslf, you should not have started the takeoff roll if you knew that there was wildlife in the runway environment or if you knew you couldn't follow your normal takeoff procedures.
I recommend reading this publication:
TP 13549 - Sharing the Skies - Transport Canada
Specifically in this chapter (
Chapter 10 ? Solutions ? Pilots - Transport Canada) they discuss that you would be in violation of CAR 602.01 "Reckless or negligent operation of aircraft".