In my Old Testament and New Testament courses in college, I was led to believe that the conflict between Jesus and the Pharisees is largely thought to be from later Christians reading their own disputes back into the time of Jesus by writing the gospels in a way reflecting current concerns in their own communities. I know that some people have thought this (e.g. as diverse scholars as E.P. Sanders and Jacob Neusner, usually on opposite sides when it comes to the history of rabbinic thought), and I never myself thought there was evidence for this, but it surprised me to encounter a discussion of this this morning that shows the scholarly consensus on the matter to be moving in exactly the opposite direction. Here are some of the reasons they're moving back toward a traditional view on this.
One of the few positive evidences for the view in question is Josephus' slim emphasis on the role of the Pharisees, but recent scholars have given some apologetic reasons why he might have deliberately downplayed their role. The main reason seems to be that Pharisees were not the primary enemies of Christianity from the late 40s through the 60s. However, the gospel accounts are not about that period but about the early 30s. Is it possible that the Pharisees had a more negative attitude overall toward Jesus during his lifetime but then became influenced by more tolerant Pharisees some time after that, with only some opposition by Pharisees in the intervening period (as Phil 3:5-6 evidences, and this is quite consistent with the book of Acts).
So the evidence is basically as follows. The opponents in the Jesus traditions passed down to us don't match up with main opponents of the beginning of the church years after the time of the gospels. One would expect that if the early Jesus traditions were modified by anything it would first and foremost have been skewed by the opposition during that period, which was primarily with those associated with the high priestly/Saducee group. Jesus' teaching more closely resembles Pharisaic teachings compared with the other major parties of the time, but there seem to be three independent corroborating traditions about conflict between Jesus and the Pharisees over sabbath issues (Mark 2:23-28; Luke 13:10-17; John 5:1ff.). Conflicts within a group or between similar groups with a basic set of shared values start more easily than conflicts between diverse groups with different assumptions.
None of this shows anything without a doubt, but the reasons for thinking Pharisees were fairly innocent or uninvolved until after the temple's destruction are out of step with the rabbinic tradition anyway. The most plausible explanation to my mind of the origin of the synagogues is that they arose not from the destruction of the temple (and therefore the end of sacrificing) but out of the necessity of continued worship during the exile (similarly with no sacrificing). The returned exiles would have continued the focus on prayer, singing, and study of the scriptures even with the second temple, and the synagogue model took hold in more remote parts from which people went to Jerusalem only at major festivals. The Pharisees seem to be in the direct line of this sort of study, which often led to good things. Unfortunately, as with any group wanting to preserve its distinctiveness when others sacrifice crucial elements, the Pharisees would likely have tended to emphasize their distinctives over the commonalities with other groups, which would be the origin of what Jesus criticized so sharply -- what we now call legalism (emphasizing the letter of the law even when it opposes the spirit of the law).
The early Christians, post-resurrection, could see Pharasaic belief in resurrection as a way to seek their support or at least their tolerance when other groups, like the Saducees and the priestly class who supported them, who didn't look forward to the resurrection at the end. Paul made good use of this conflict during his trial before the Sanhedrin, saying that it was a Pharisaic belief that he was being persecuted for. A number of Pharisees, despite their sometime role in persecuting Christians (as Paul did), expressed more tolerant attitudes, and perhaps this dominated until after the temple's destruction. So there's a perfectly good reason why the Pharisees might by and large have changed their attitude toward the Christian sect, and then the standard account resumes the story with its description of how things went after AD 70. It's just that it seems well beyond the evidence to say that there must not have been a Pharisaic opposition to Jesus before the issue of resurrection would have led Pharisees to see Christians as allies against the Saducees.