It should first be noted that the k'thiv/q'rei phenomenon you refer to is only observed in the Pentateuch and not elsewhere in Tanach. That being said, there appear to be two major camps on this issue. One camp believes along the lines of what you suggested, namely that הוא was actually written to mean היא. The explanation is that waw and yod were used interchangeably when writing the third person pronoun. If you think about it, a waw is basically a yod with a longer stem. So even though הוא appears to be the same word, it actually represents both forms. The forms הואה and היאה are found in Qumran texts. Here is a source from this school of thought:
The Bible and the Dead Sea Scrolls, Charlesworth
The second school of thought is that there is no k'thiv/q'rei occurring. The explanation is that one gender-neutral form for the third person pronoun existed in a more ancient form of the language. This form would be written as הא using Hebrew lettering. When medial vowels were introduced into Hebrew at a later stage, scribes erroneously extended הא to הוא throughout the Masoretic text. One argument for this school of thought is that Moabite and Phoenician inscriptions have been found bearing the early form of the pronoun הא. A second argument against the k'thiv/q'rei argument is that this variation occurs 120 times in the Hebrew bible. It would therefore seem unlikely that these are random scribal errors. Here is the source for this school of thought:
A New Look at Pentateuchal HW' *, Rendsburg
