Well, off the top of my head, there are a few things.
Last edition you re-rolled if you got a power beyond your master level, but in this edition that isn't the case.The main reason is that many of the tables include ML2 and ML3 powers, which is just going to end up causing people to roll powers they can't even realistically cast. So you will need to further alter the core game to deal with that (I guess it would be you are only able to roll powers you could possibly cast with the ML+1 ruling).
Generally, you need 4's to succeed on psychic tests and 6s to deny them. Any Mastery Level 1 powers don't take much of a hit; you only need one 4+ to get the power off and rolling two dice is fairly safe and will probably be common because of extra warp charges.
The ML2 and up powers suffer more. To reliably cast a spell with 2 Warp Charges (some of which are popular, like Prescience), your ML1 psyker can still try but needs to pass on both dice. I don't know strict percentages on this, but if each die has a 50% change of being a failure, it seems pretty unlikely. Adding the third die adds some insurance, but not much.
The ML3 powers really take a hit. Only the most heavily upgraded psykers can even attempt them, and with 4 dice and needing 4+ on three of them, they are unlikely to even work a decent amount of the time. These powers also were previously balanced out by the risk of more dice meaning more perils, so there will be less Perils of the Warp instances as well.
Also, probably a huge amount of Warp Charge will be pointlessly wasted every turn. Even in an army with one ML1 psyker, it is potentially a pool of 7 Warp Charge, which he can only use 2 of.
Finally...this doesn't really resolve the (perceived) problem, as the Conjuration to make new Heralds with awesome wargear options for free is only Mastery Level 1 and can be cast pretty easily by any Joe Schmoe anyway. So you would just end up with a table full of AP2-toting Heralds with Greater Gift rolls making them beefier upon being born. This is probably worse than the million Bloodthirster problem because each of these guys is a psyker in their own right a lot of the time, and can also be represented by a slightly different standard model (which, as far as your concerned, means a player could technically buy a ton more "Heralds" with ease - 10 to a box, prime a different color, "the blue ones are heralds", and voila...). And because it's ML1, you can attempt this power very safely, as you can't perils on 1 die.