I've been doing missions for then until the point one of then asks me to find a certain girl. At wich point not knowing what he wanted with her since he would't tell, i went and found her, only to find a quest with her, wich showed me they weren't all that big of saints. I went with the peaceful solution, but now the cryer and guard on the entrace both attacked me, and when i try to get inside they shot me.

I wasn't planning on bringing the girl in the first place, after i found out they were going to kill her, so i popped a stealth boy, and started to snipe then from the entrace. And now i'm left wondering if there are any draw backs to killing all of then besides the loss of the weapon store (not really that much of a problem since i use normal guns).

Also, how come they are not viewed as evil, even tough they kill any competition?

Apart from a questline, money and a EW store?
Nope, no drawbacks.

First of all, regarding the girl Cass, if you talk to her after she's hired and do her quest (Heartache by the Numbers) things will come full circle and you'll find out why the Van Graffs want her gone.

Second of all, there's no real downside to killing the Van Graffs, it's more a choice of one path or another:

1. If you are an Energy Weapons player they are the major vendor but that is not really a downside. If you kill the Van Graffs you get to loot their store and get the best energy weapons for free, and all merchants in the Mojave sell EW ammunition, so it's not a drawback.

2. Regarding other quests, you may lose the Van Graff quest but the girl Cass also has a questline of her own (Heartache by the Numbers) and if you choose one path you cannot choose the other. I don't see that as a drawback it's just a choice of doing the quests for the Van Graffs or doing the quests for Cass.

3. Regarding evilness, the game has a lot of inconsistencies with Alice McLafferty, Gloria Van Graff and Jean-Baptiste Cutting being shining examples of the inconsistency. All three are technically neutral in alignment which does not sync with the story. You get the full story behind the Alice-Gloria-Jean axis of evil if you do Cass's quest (Heartache by the Numbers). In any case, good and evil player karma has very little impact on the game so it's not that big of a deal. Probably it was an areas the developers would have liked to make more use of but didn't have the resources to flesh it out.

If you kill the Van Graffs the only other Energy Weapon store will be the Brotherhood of Steel. However, if they are both destroyed the Gun Runner Vendortron will sell their energy weapons. But be warned. It is a confirmed glitch that the Gun Runners will not sell their stock after they have been killed.