I'm looking for some tool that can help me but I don't know if this exists. What I would like to do is to be able to convert the output of for example Google translate to a sentence that contains the hiragana for Kanji written in  after the kanji.
This PDF describes some of the difficulties in ascertaining how to read the two-kanji name 淳子. This might provide some hints as to why such a tool is ultimately an impossibility.
Even if we ignore proper names (since these are notoriously variable in Japanese), we find strings like 金山, which could be read variously as かなやま, きんざん, or こんせん, depending on context.
Ultimately, I don't think such a tool exists. If it does, its capabilities are probably restricted to those sets of kanji-spelled words that have
single unambiguous readings.
Unfortunately getting kanji readings right is not an exact science, but you can get some approximation by using the text glossing feature in WWWJDIC (and few other similar sites/apps). You'll likely quickly see missing or wrong readings for many kanji combinations.