May I suggest my own PinyinTones IME, which does exactly what the OP was looking for:
It's a Windows IME that outputs Pinyin with tone marks, rather than Chinese characters. Type 1, 2, 3, or 4 after each syllable to add a tone mark -- just as people have been entering Pinyin since the days of ASCII characters:
Uses the Text Services Framework, so it works everywhere that the Microsoft Pinyin IME works. Including Windows 8 -- desktop and Windows Stores applications.
Uses in-line text composition, just like the Microsoft IMEs. This means that it behaves well in TSF-aware applications -- for example, when inserting, text will reflow as you type.
Automatically places tone marks on the correct vowel in a combination, according to the rules of Pinyin orthography. (e.g., hao3 becomes hǎo -- with the tone mark on the "a" rather than on the "o")