[Klashikari]

It isn't really a matter of being "slapstick" or not. Hell, Masato and Kengo combined with Rin and all is still slapstick, but it didn't particularly make the discipline commitee acting against them (with few exceptions such like Masato and Riki entering in the girls' dormitory).
The problem was however stated (not exactly shown that well) by several characters, be it the commitee or other characters like Masato: whether or not Haruka's pranks aren't that of a major problem that lead to lasting consequences, she is a recidivist in her practices, and even defy those who are supposed to do their job, albeit overzealously.

Picture it yourself: I can't see anyone letting slide someone's prank when it is repeated countlessly even after several punishments and lecture (I'm not talking about the extent of Haruka's pranks per se, but rather how often she is bringing troubles for no real reason).
Kiljoy or not, there are rules to be respected to a certain extent, and whereas not every students can pretend to be completely white in that regard in a general sense (be it seriously or in a laid back anime sense), it is natural to have a "bias" when it is just repeated.
In a purely comedy show, you have such antics as the norm and a commitee like that are also played for giggles as either the straight man or the antagonist. But in LB case, it isn't a purely driven comedy show, so you have a sense of balance in term of mood and events.
Heck, Masato who is often the receiving end of many characters' "physical abuse" just can't stand Haruka's nagging approaches, despite Rin dealt much more pain to him than Haruka.

Simply speaking, expecting Haruka's actions as normal and "okay" because it is played for comedy doesn't really work as LB isn't something akin to any pure slapstick show.
It is also why her reputation is known as troublemaker and it isn't only the discipline commitee, but also other characters (even nameless ones, but that wasn't shown in the anime). In fact, most characters often jump on the gun when some troubles arise, thinking it is Haruka's doing (except when it goes serious, such as the vending machine incident, which was motivated by the commitee bias).

Note that I do not state that Kanata's behaviour is level headed by any means, but the commitee decisions and stance are rather "normal" given the circumstances. Harsh with mean remarks due to bias? Sure. But irrelevant/unfounded? No.

Regarding what she says to the LB, bear in mind that her comments are done due to specific circumstances.
-The first time was a warning due to furniture damage, which is considered as vandalism. No matter how funny it was, you can't discard that the LB were careless about it.
-The second time was Riki and Masato in the girls' dormitory. Of course, you can say that Masato and Riki didn't have any ill intention, but at the same time, they could simply ask girls to help Kud by the entrance.
-Kanata's remarks regarding the LB are hardass sure, but are based on their antics: surely battles on school grounds, even for the kicks aren't really what you would expect and it is well known as a good number of students watch the battles and even assist to the weapon selections. As such you can't expect a discipline commitee to let slide a bunch of kids putting a show like that.
Also, she took action against the girls in episode 15 only when it really went out of hand with their ruckus, to which could have been done much earlier.

Also note that due to the rules, Kanata could also jump on them for the cafeteria incident, especially there was no way for her to not know the LB took action for that, yet she let it slide.

So really, circumstances regarding her approach to the LB isn't exactly that affected by Haruka's presence.