It's hard to say without seeing the quilt, but one thing to consider is that if you take a dart in one direction, the other direction may still have that fullness, and that will mean the quilt will be difficult to quilt and will not lay flat after quilting. I know it sounds like a lot of work, but it might be worth the effort to take out a few rows and correct the original problem (the size of the blocks) rather than try to fix it from a later point. You are very smart to fix this before you add the borders.
My first quilt was a simple Yellow Brick Road (YBR). The blocks weren't all the same size, so when I sewed them together the quilt was wonky and didn't measure even close to square. My teacher, who is generally pretty tolerant of errors and short cuts, agreed that I needed to take it apart and fix the blocks that were off. You are not alone!