The writers acknowledged that they are entirely aware of the subtext they infuse in virtually every episode. That's correct. They know what they're doing, and they're doing it on purpose. These are the reasons they gave my class:
1.) They want parallel the relationship with Holmes and Watson. This is not to say that they believe Holmes and Watson were necessarily "romantically involved," but that they wanted to mirror the level of trust and loyalty between the two. It's a relationship that goes above and beyond the categories of friends and lovers.
2.) They have seen the rampant fanfiction online, and they know the slash circle is quite large. They do not want to exclude us as an audience. (And besides, a handful of the writers on staff are on our side anyway).
3.) Admittedly, the House and Wilson relationship is the most important relationship in the show to date.
They made a disclaimer, however, that the Cameron/House relationship will come into play more later on. Unfortunately, they did not divulge any further information about how or why as that would spoil their plans for season 4. (Something for the H/C people to look forward to).
David Shore said that the fall-out between House and Wilson is temporary. To surmise what he said (to the best of my memory): The fall-out has to be temporary. These two characters combined bring balance to the show's comedy and drama.
When they pitted Wilson and House against one another, the balance was disrupted. This is evident through the tonal shift of season 3. The season suddenly became dark (darker than they intended), which is a testament to what happens when Wilson and House are not on a friendly basis. They had to test the friendship for the sake of House's personal growth as a character. To do this, they had to break away from the formula they set-up in seasons 1 and 2, even though that risked upsetting the audience. Quoting Russell "we valued House's growth more than p*ssing off the audience."
Hope you enjoyed this as much as I did. They talked about the H/W relationship for about 15 minutes. The remainder of the two hour lecture focused on how the show got started, how they plan on gradually serializing the story arcs, etc., and the writing and producing process.