Question has come up before in games and we have made a ruling, but I would like to get the opinion of other people to see if its correct. 

The rules for blockades are simple, A square in a city’s outskirts that contains one or more enemy figures (either scouts or armies) does not generate production, trade, culture, coins, or resources for the city’s owner.  

Obviously you can deny the owner of the city the trade provided by the buildings, but the +2 or +4 combat bonus is not mentioned in the above rule.    Because of this, my group and myself have ruled that you cannot blockade the combat bonus from the buildings or great generals. 

What are the thoughts of the other players?  

Check out this: http://boardgamegeek.com/filepage/65536/unofficial-faq

I actually sent in a rules question about this once and the official reply boils down to the following:

You may blockade academies and such, preventing their owner to get the military bonus, but if you do so with a scout you do not gain said military bonus(es).

Really?  Interesting.   This actually goes against the unofficial FAQ (from KW) that I read in the above link.    

Well I really hope they make an updated FAQ soon. 

Well the term "unofficial" does somewhat lessen it's credability rating in my eyes.