Bruce Timm grew up with Batgirl being closer in age to Batman before they aged her down to be around Dick's age (supposedly to get him away from Starfire and the Teen Titans depending on what theory you subscribe to) so it probably wasn't that icky to him when you consider the relationship from that perspective. Gordon also isn't really Bruce's "friend", he's already generally a senior citizen with a teenage daughter (or niece depending on the continuity) by the time Bruce starts Batmanning in his 20s.
It's still distasteful the way Timm does it but there does exist a precedent for this.
I will say with their paring in particular most of my problem comes down to the fact we have had the status quo we have had with them since the 80s pretty much ever since, and it ends up weird to put those two together.
if we're not doing the basic familiar modern batman status quo, I wouldn't really care. in that movie they tried to do something interesting with her, but it imo ended up making her feel like even more of just a sex object to me, because it's like Batman fucks her, then look now Joker made it so she can't (enjoyably? I guess) fuck anyone. I get what they were going for with it, it just didn't play.
that movie I already thinks sucks even when we get to the killing joke portion, because it doesn't really look like the killing joke. which, shit, buy a copy of it off the shelf, the book doesn't even look like the killing joke anymore with the modern recolor but Bolland did that himself and says he prefers it so whatcha gonna do?
As for the Gordon/Bruce brother thing, their typical ages is sort of irrelevant to me because they're both lonely men with basically each other as their only friends and have more of that type of dynamic then Bruce looking up to Gordon as some sort of father/uncle figure. I'm not a lonely man with one friend who isn't my adopted dad or in Gordon's case one friend who isn't my fat slob coworker, but just because a friend of mine is like 50 and I'm 30 doesn't make them less of a brother in my eyes and more of something else.
but most of that is just hyperbole anyways and just in my personal mental version of the Batman world they're more like brothers, whether they're 10 years apart or 35.
but the thing about Batman and his world is I can pretty much take whatever with it. It's more malleable than a lot of franchises to me where you can shift tones styles and dynamics pretty much however the fuck you want and as long as he dresses up like a bat and punches people somewhere in there I'll accept it. You can give me Dick Sprang or Frank Miller and I don't give a shit it just has to be entertaining.