He's also
reported as saying - a bit more specifically - that as far as *this* movie (meaning AOU) is concerned he's dead (but also that bringing him back for Agents of SHIELD was a 'no brainer'). I don't think it's a leap to assume that he's meaning that in AOU it simply wasn't the right time to have that revelation.
Also, ultimately, Whedon is not the end-all-be-all of what will and won't be in future MCU films - his opinion (whether he misspoke or not) is just his opinion. Coulson is alive in the MCU because Agents of SHIELD is a part of the MCU. This is an indisputable fact and one that Whedon is well aware of since he helped bring Coulson back. The question is only when the revelation he's alive might be revealed to the main superheroes of the MCU franchises. AOU wasn't the time to have that happen. Nothing wrong with that.