It's quite pretty there. Sure, there are Muslims there; one would be hard pressed to find a country without them at all these days. Heck, I was in Venice and (1) there were mosques and (2) there were Chinese restaurants. Malaysia is no different.
Anyway, the people are very nice, and regardless what their outgoing PM keeps saying about us Amurricans, the people love us. I never met anyone "on the street" that outwardly displayed any issue with whitefolk. Remember, they're close to Australia, and recieve many, many foreigners a year visiting the resorts there. I'd pick Tioman (in Malaysia) over Bali any day personally.
Kuala Lumpur is just a big city. And like any big city, has its pros and cons. It's a congested and crowded concrete jungle with some strategically placed trees. The food is wonderful, however. You can get most anything you want in Kuala Lumpur. Fast food? McD's and the Colonel are everywhere. Steaks? Plenty of "western" steakhouses around. They even have Chili's and TGI Fridays, so no, if you're worried about food, KL is not one of those places to have this worry.
If you want to venture into the local cuisine, I suggest you go to one of the countless 5-star Hotels. They serve the authentic local cuisines as well, but at western prices. The benefit there is the hygene is guaranteed. It's hit-or-miss at the local food stalls although the latter is quite a bit cheaper. My wife didn't take too well to one dish she tried from a food stall. Nothing serious, just an upset tummy, but it scared us both for a whole day (now where do you find pharmacies, and what do they call them ... oh! they're called Farmasi's!!)
I'd say go for it. You will have a good time. If anything, you might be a bit disappointed it's not as "backward" or "exotic" as you'd expect it to be.