First of all, please put Fate/stay night in a spoiler box.
About the Sumika stuff; You're not exaggerating. A lot of people would consider it to be very extreme, especially those who are not used to that sort of thing. One could argue that it's a very effective way to make the player hate BETA, but on the other hand, there are a lot of other ways to do that without (tentacle) rape. It seems to me like JP VN writers tend to use rape often, nukige aside. It's sort of commonplace in mecha and/or more serious action VNs. I can name quite a few high rated VNs that I haven't played yet which most probably have some form of molestation or rape. It's kind of odd to say, but you'll get used to it, probably. :/
Personally, I don't like pointless rape scenes that are used randomly, just for the hell of it. If these scenes are present, at least it should make sense in that story/situation. MLA can get away with Sumika's rape scene in my opinion. I would probably be traumatized by it like you are if I wasn't used to it already. ^^
By the way, if you want to chat about MLA or other VNs, etc., you can always come to the Shoutbox chat on this forum. I'm pretty sure most of us who chat there already played MLA.