The Walford show has received a public backlash over a plot which has seen Ronnie Branning (Samantha Womack) lose her baby son James to cot death, before secretly switching him with Kat Moon's (Jessie Wallace) child in her despair.
Writing on the official EastEnders website about the row, Kirkwood commented: "Our aim was - and still is - to tell a strong story that would, in the telling, raise the profile of cot death in the UK. It's clear that we've managed to do this, and that traffic to the FSID [Foundation for the Study of Infant Deaths] website has increased by over 500%, but we are also mindful of the fact that in doing so, sections of our audience have found the storyline challenging.
"EastEnders never sets out to upset its audience - not only would it be counter-productive, it would be a breach of a long-established trust that we can deliver truthful stories that inspire debate in a way that's acceptable to a family audience.
"Although we have had complaints, we have also had positive responses from people who have been through the experiences we are currently dramatising who feel we've done this and have contacted us to offer their backing.
"A large portion of audience are watching and being supportive of the storyline so we owe those viewers the opportunity to continue to engage with it and see the storyline through to its rightful conclusion."
Kirkwood also discussed the now-confirmed decision to end the storyline early. Reports suggest that it could conclude on screen by April.
He said: "Whenever we embark on a story at EastEnders, we always leave it open-ended to monitor and listen to audience reaction. With this in mind, we are going to bring the story to a close on screen in the spring.
"As the story progresses and Kat is reunited with her child, we hope to explore the impact of the tragic events that have befallen the characters in a way that is powerful, but true to the best public service tradition of the show."