The place it really becomes a problem (and this would be worse for Chinese than Japanese because Chinese is 100% kanji) is when you have a kanji that has an extremely common pronunciation.
You are doing it wrong. If you type in pinyin for a common character, sure, you will get a hundred choices. But you should just ignore those choices, and keep typing. After you type the pinyin for a string of characters, there is usually only one valid interpretation. For instance, if you type "qing" you will get a hundred choices. But if you type "qinggeiwoyigepingguo" (meaning "Please give me an apple") you will get ONE choice, and it will be the correct one.