Why microwaves do not kill harmful bacteria as well as boiling?
I'll go ahead and take a stab at answering this, even though the question is a bit vague. I assume by "cook" you mean "cook with a non-microwave method", like boiling, steaming, baking, frying, sauteeing, or anything else.

First of all, no, I can't think of any reason why microwaves would be worse than any other cooking method. If you fully cook something in a microwave, it is as safe as fully cooking it any other way. If the food reaches the same temperatures, and is held there for the same amount of time, the bacteria will be just as dead no matter what the heat source is. The heat supplied by a microwave is fairly similar to that supplied by steaming, and no one claims that steaming is an unsafe cooking method. The only thing I can think that would be unsafe is if you don't actually fully cook the food, but just heat it to the temperature that you want to eat it at. But that'd be a problem for any cooking method; dangerous undercooked meat is dangerous because of the temperature, not the cooking method. (And of course, not all food needs to be cooked to be safe.)

The arguments you suggest don't really make much sense to me, either. For the first, I don't have any idea what you mean by heat frequency or sequentially different waves; heat is not a wave, so I'm not sure how to respond. No matter how you're cooking something, heat is being transferred into the food. Heat caused by absorption of microwaves is no different from heat supplied by contact with boiling water, steam, pan, or the hot air in an oven. It's still heat transfer, and it makes the temperature go up. Different methods may heat more or less evenly, or at different speeds, but heat is heat.

As for your second suggestion, reflection of microwaves, well, that happens already. You may have noticed that the food in a microwave ends up hot on all sides; this is especially noticeable if it's a big solid piece of food like a casserole. It'll be hot on the top, the bottom, and the sides. The microwaves are reflected around; there's really no other way for it to be. If they weren't reflected they'd have to either be absorbed (meaning your microwave would heat itself up) or pass through the walls (meaning standing next to a microwave would be dangerous). And it'd be horribly inefficient, on top of that.

Of course, all the stuff about reflection and heating from all sides is still a moot point in terms of food safety. When you cook something in a pan on the stove, as long as you fully cook it, it's fine, even though it's only being heated from the bottom. All that matters is the temperature the food reaches.