That's the way comics were written back in the day, the way all sci-fi and fantasy works. You cloak the issue you actually want to address in tights and a cape, so that people are distracted by the outer covering while the internal issues creep in unnoticed.
I seriously doubt that Bob Kane or Bill Finger were thinking of this as a homosexual metaphor. Really, it was just a case of trying to do a modern day "Zorro."
Most of the allegedly homosexual subtext in the old Batman books was obviously a combination of changing word meanings (for example, "queer" and "gay" meaning "strange" and "happy" back then) and the fact that it was written for little boys who wouldn't be caught dead reading about kissing "yucky girls" and to whom wrestling and sleepovers was still asexual.
I'd also point out that, if secret identities and kid sidekicks are automatically [metaphorically] gay then pretty much every comic book superhero ever written pre-Fantastic Four, including Superman (and Jimmy Olsen), is just as [metaphorically] gay. So, unless Morrison thinks they're all
[metaphorically] gay, it is just another example of him not understanding Batman and taking the cheapest and easiest, Schumacheresque, analysis of the character available as his hook.
If anything, golden age and silver age Batman is about arrested development and extended adolescence: a grown man who suffered a trauma as a child who spends his life playing with "toys" from the batcave and having adventures with another kid, while doing his best to eschew his "work" (Wayne foundation) and family responsibilities and having an older parental figure still taking care of him.