It wasn't a huge problem, but it was a mistake they made. They never intended for it to function that way. Similar to when they accidentally made it so that the harlequin horn and gjallarhorn changed chocobo mazurka to flee speed.
Both were unintended buffs which made certain jobs stronger than they were intended to be, so SE immediately patched them. The difference, of course being that mazurka giving flee speed is a big unfair buff to a job that is and always has been desirable whereas sambas affecting pets still was not enough to make pet jobs useful enough to consider for endgame.
I fully support the changes requested in this thread. The way the game currently functions, having the right buffs and gear are how you deal the big damage. Pets have minimal gear available to buff them, and that gear requires the master to sacrifice their own damage potential. Pets also have minimal buffs available to them, and no sane cor would give bst roll over drk roll except in very specific situations. So the bottom line is that pets do not get buffs which all players require to be at the top of their game.