The more I've thought about it after you mentioned it on the stream, removing the runes from the reward track should be a non-starter, as all of your paid pass players have already paid for the chance to get them. So removing them is scammy, and possibly illegal in many countries (bait and switch in online purchasing of virtual goods). I would strongly encourage you to drop this path of exploration. There is only downside.
That said, you have plenty of tuning knobs available to you to address the concern than players feel those rewards are out of reach.
One is increasing point rewards, which moves players along the reward path quicker (and only last for this single season, so is not a permanent condition).
Or, moving the more desirable parts of the post 50 reward track (e.g. Rune stacks) to the 40-50 range and having post 50 be only mats. Either of these addresses the problem, without creating a new one of very unhappy paying customers.
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