Voting against it is just saying we are not accepting the ref result and will keep fighting it (hopefulness or otherwise).
No, it would be disagreeing with leaving the EU. It is not possible to argue with the result of the referendum. The result is fact. It is still perfectly possible to argue that leaving the EU is a bad idea. If that were not possible we would be living in a dictatorship that did not allow freedom of speech.
The reason that a majority of MPs will support leaving the EU is that it would be political suicide not to do so. If a majority of MPs had constituencies backing staying in the EU, they might try to block leaving, but in a situation where the popular vote were at odds with parliamentary representation, leaving the EU would look very uncertain anyway - it is likely that the vote would have to be clarified further e.g. by general election.
After each general election, the opposition loses but can vote against government policies with which it disagrees. They don't lose their voice, just the ability to pass legislation and form a government.
Had remain won, it is perfectly possible that the UK would have left the EU in the next decade, just as the Scottish referendum does not mean that Scotland must stay part of the U.K. for eternity.
It would be harder to re-enter the EU having left, but people are at liberty to continue campaigning for it and political parties are free to represent them.