There's no chance Kovalchuk made more on his KHL salary than he made on his NHL contract over the last five years. As mentioned, there still is tax in the KHL, and his salary was literally double his KHL salary through those 5 years. Even with zero tax planning by Kovalchuk and accepting the 50% effective tax assertion, he would have earned more in the NHL.
A few things here:
-It's hard to gauge what Kovalchuk was really making in the KHL, since just about every report seemed to note that bonuses were not included.
-If the players are taxed at all in the KHL it's likely closer to something like 13%
-The other factor you're forgetting is Escrow in the NHL. When Kovalchuk signed that deal, players were getting most of their Escrow withholdings back (4.1% withheld in 09-10, with 3% returned). That changed after the last lockout, when the withholdings went up, and returns went way down (16.3% withheld, 1.6% returned in 2012-13). Based on the reported withholding and return for the next couple of seasons, in addition to the supposed 50% tax, he would've lost $1.15M for 13-14 and $1.46M for 14-15 through ESCROW.
-Even if he did make less on his KHL salary than he would've in the NHL, his profile in his home country is probably much larger, likely opening the door for many other ways to line his pockets.