I believe it was also due to wanting developers to make use of the latest OS frameworks. Third party development frameworks often lagged behind in features (i.e, doesn't support new auto rotation features, doesn't support new camera features, and so on).
The policy was changed and ultimately never enforced, but I always viewed it as a way to ensure that developers kept up-to-date.
It think the timing (days before the Adobe Flash CS5 launch, the first release that included iPhone application support, IIRC) and the eventual reversal makes it clear that this was about making life difficult for Adobe and Flash and not much else.
The policy was changed and ultimately never enforced, but I always viewed it as a way to ensure that developers kept up-to-date.