The phrase, in my head, is short for "I will pencil you in for a meeting on Sunday". The words "a meeting on" are omitted as implied.
Using "on" changes the meaning of the phrase; "I will pencil you in on Sunday" implies that the speaker will actually put the entry in the appointment book on Sunday. Perhaps they're away from home and won't have access to their datebook until then. Perhaps they won't know whether there will be a conflict until then.
So, the use of "on" is valid, but results in a very different meaning than the one normally implied by the use of "for"; in that case, the speaker is saying they will tentatively add the appointment, which would occur on Sunday, to their book at some indeterminate but probably very near-term time.