Plain and simple, he's (now) trying to cover his own ass, so to speak...
Definitely possible.
And it's hurting the prosecution's case. If he's the main witness, he's not helping his credibility.
OK simplest assumption, both McQueary and Paterno told the truth to the Grand Jury (penalties of perjury and all that)
Originally McQueary witnesses the rape and runs away distraught. Two days later, when he goes to see Paterno, he realizes this wasn't very manly and minimizes what he saw "something odd, could have be shenanigans, maybe just horseplay". Without a firm statement from McQ or the unknown victim, all the University can do is put Jerry on double secret probation.
Fast forward seven years, after anoter parent complain, real law enforcement reviews Sandusky's history and find out about McQ's talking to University authorities in 2002. The subpoena him.
McQueary doesn't know why he's being called. Maybe the 2002 kid's come forward, in which case "I wasn't sure what was happening" isn't going to fly. So, not knowing what the GJ already knows, McQ takes the safest course and tells the exact truth.
This doesn't put him in a good light, hence the backtracking, there being no penalty (as yet) for lying in e-mails.