Morsy is now trying to mobilise the revolutionary vote for him, and some (like the novelist Alaa El Aswany) are going along with that. But everything that the Brotherhood has done in the past year and so indicates that as soon as they gain power, they will drop, marginalise, and - if necessary - recklessly repress their former allies.
However tempted by an anti-Shafiq, pro-Morsi, vote, secular / progressive / revolutionary voters are in the second round, how many will actually do it in light of their perception of the MB's behavior in the last year? This is what the Brotherhood lost by some of its behavior over the last year, notably over the constitutional assembly and its refusal to seriously condemn crackdown on protestors: its claim to the leadership of the opposition. This is why Morsi's score, in most interpretations of the results, is seen as being against both the old regime and the revolutionaries: the Brotherhood is perceived as forming its own distinct group. Indeed, the prospect of a restoration of the old regime through Shafiq is not necessarily as terrifying to some to an unstable military-Brotherhood alliance like Sudan in the late 1980s (see how that ended?)
It is a tough dilemma: one might be tempted to block Shafiq by voting Morsi, but then think that Morsi will just turn around and negotiate with the army without any input from the "revolutionary" forces. I spoke about this to MB leader Khairat al-Shater the morning after the election; he seemed to think there was no need to bring in other candidates as VPs or promise them cabinet positions (or some policy impact) because even if their voters did not choose Morsi as their first choice, there is a reservoir of goodwill towards the MB among them.
But that's not how politics should work: candidates' endorsements should be in exchange of clear gains, most notably an actual position of influence in government (and in that case VP may not be the job to go for). Discussion of this in the Egyptian media makes it seems like it's some kind of dirty deal, but that's BS: the unlucky candidates that represent about 50% of the first round vote need to get something for their support.
Update: While I think Hamdeen Sabahi should focus on his appeal for a recount and try to invalidate some of the Shafiq votes for now, his statement that he refuses any position under Morsi is non-sensical. The question should be what does he get from them — both personally and hopefully for what he thinks his voters represent.