Both of your phrases use an infinitive form of the verb wait. The first uses the ordinary infinitive:
It is not acceptable to wait for...
In your second phrase, the verb be is used to form the progressive infinitive of the verb wait.
It is not acceptable to be waiting for...
We use progressive forms and tenses to talk about conditions or actions that are (or were, or will be) in progress at the time we are talking about.
It is sometimes idiomatic to use the progressive infinitive to emphasize the action that is described by the verb. Compare:
It's about time for us to be going.
It's about time for us to go.
Isn't it a little late to be driving?
Isn't it a little late to drive?
It is not right to be bothering him like that.
It is not right to bother him like that.
There is little difference in meaning between the two phrases in your example, and very often the progressive infinitive, especially in the present tense, does not add anything to the sense of the verb.
StoneyB's answer to a related question here may also be helpful.