When Shartan helped Andraste there was no Chantry, just the prophet herself and the Chant of Light, the moral precepts of which Shartan and his followers probably had no problem with. Now when Merrill and Sebastian are discussing their respective religions, it is Sebastian, chantry boy through and through, who suggests that the elves story about their gods abandoning them and the Chant of Light talking about the Maker doing the same may both be referring to the same divine force. If Sebastian could see it this way, is it not conceivably possible that Andraste did the same? So the elves felt perfectly entitled to set up their new nation on that basis.
Then along came the Chantry, a religion set up by the Emperor Drakon of Orlais, not Andraste herself and the elves say, no thank you, we'll stick to what we know. Shortly after there comes a second blight which hits Orlais first and presumably in view of their alleged unwillingness to help did not affect the Dales at all, even though given its position, should have borne some of the brunt of the invasion. If this was the case, would not the elves think that perhaps the Maker/elven gods did not approve of this new Chantry religion being promoted by a new human empire, whose symbol is a dragon, the symbol of the old gods of the Tevinter. So then the elves continue to repulse any missionaries and are aggressive towards this new sacriligious empire, where both rulers and chantry hold their position "by divine right". When the elves attacked the Orlesian cities, may be they thought they were on their own "Exalted March". At the very least they probably thought that offense was the best form of defense against this new imperial threat.
So, no, the elves were probably not entirely innocent but since history is always written by the victors, the Orlesian/Chantry version of events is not to be trusted either.