Differently? How? Honest question: What's wrong with apologizing and expecting the users to understand there's nothing else they can do?
How many times have we heard that sentence and thought that the speaker was not sincere at all? Now, when a somebody uses it, all those insincere utterances will come to your mind with all the accompanying bad feelings.
It is good to see people apologising for inconveniences but, please, take fifteen seconds to think of a sentence that does not sound like a canned reply.