Krejci's contract is actually worth 3 mil for 1 year. It's 1 mil in base salary and 2 mil in performance bonuses. He has already earned 1.5 mil of the performance bonuses and he's a lock for the rest.
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But even if it were only 1 mil total, I doubt the NHLPA would care, as these types of discounts are much more the exception than the rule. One player taking less means another player can get more, or another player who might not have gotten a contract now gets one. The players' total slice of the pie is set. A few players taking discounts doesn't impact that. And even if the NHLPA did have an issue with it, there's nothing they could do about it.