If Fdev doesn't fix this, this will also differ in a couple of critical and dangerous ways from past "sanctioned exploits".
The PvP community successfully established norms against the use of heat cannons and heal beams. With certain notable exceptions, these norms are followed within the PvP community. The establishment of these norms was made easier by the fact that few people bothered with beams and cannons before Fdev created exploits for them. When heat cannons were finally nerfed, an entire group known primarily for exploiting them simply vanished. Healbeam use in PvP remains rare and only done by certain elements.
But frags and seekers are both very common weapons. Drag munitions in particular are already the most popular secondary for seekers and pack-hounds. That is because the effect they previously had was already quite useful. It forced CMDRs to RELY on boost to continue with fast movements, often requiring the diversion of power. It was already a useful effect (arguably the single useful effect for seekers). Many frag users also have one drag-frag already due to its effectiveness as a ToT enhancer.
But I digress. The point is that because of the already widespread adoption it will not be so easy to establish a norm against its use. People are not likely to be willing to change builds, let alone waste any materials to change engineering.
This is likely to drive many PvPers (and likely others due to frags becoming an even stronger ganking weapon) away from the game if it is left in its present state. If I did not know better I might assume that an intended effect.
Nonetheless, there are three easy ways to at least make this a little more balanced.
1. Revert this change entirely.
2. Separate the "0-Pip" effect from the new "boost block effect" and have them be two separate special effects, ideally one for frags only and one for seekers only.
Seekers only get the boost block effect which I shall call "Dampening Munition". This blocks boost for a few seconds, has a one-minute cooldown, and does negligible damage with an extremely low (or nonexistant) breach chance.
Frags keep the old "Drag Munitions" effect as it existed prior to this patch.
3. At an absolute minimum, impose a cooldown of at least thirty seconds (but ideally, a minute) on at least the boost-blocking effect.