I think they were, it's called continuity and the film is jam packed with progression.
http://youtu.be/uKjra8i2XTw?t=43s
"Again Michael what you're suggesting is an interesting thing. You don't want to look too sluggish. You want to look wounded but you're still going for it."
There was a thought process in all of it. If there wasn't a "point" to having him be beaten, they wouldn't have bothered showing Batman limping, struggling up the cathedral steps or even bumping into one of the pews causing them all to collapse. If they weren't thinking about the previous scene, why did they care about the continuity of all the blood and shrapnel in his face? Or the cuts and gouges in his suit, or the heat seared, cracked bat chest emblem? Surely all these set pieces were filmed on different days of production.
Yeah, it is a fun scene but not because, "herrr derrr, look at Batman getting his butt kicked by a random and having to kill to win, so un-Batman like". It's a fun scene because as Batman is fighting the Joker's men, the Joker is dancing to a waltz with a hostage. It's not fun for Batman though. Those blows to the head aren't "lolz".
I mean, what card are we going to play here? "Comic book superhero Batman would beat that guy easily" or "this is a film with a human Batman that can hurt and bleed". I guarantee that the filmmakers had that in mind. It would have been quite boring if Batman dispatched of the Joker thug as easily as he did the others. Up until that fight Batman kicked everyone's ass unscathed, even the sword wielding yakuza thug.
I dunno about that. You ever been in a car accident? Your body feels destroyed in even a minor crash. Now a single pilot jet flying into a wall? Ouch. I'd take being rusty fighting wise and using my trusty magic knee brace over ****ing metal pieces in my FACE and cuts, bruises, burns and abrasions everywhere. I'm actually surprised they didn't give Keaton a scar prosthetic from the wounds that were inflicted on the character in the first film.