It's my understanding that IPSC allows it because although your modifying the safety, your emulating a gun that is allowed in production (The Julie Goloski edition)..so your not getting any advantage that the production Goloski doesn't have already. Any mod that comes from the factory is allowed.
While there would be no advantage over the other version, I think if you were to inquire on the IPSC global village, you would find that the gun being modified to remove the magazine disconnect would remove it from production division. It would still be allowed in the other divisions, just not production. Of course, if you ordered the production version that didn't have the disconnect to begin with, then you would be fine in production division.
Most local matches would allow you in production division with the modification because they would never check your gun, but if you ever went to nationals or an international match you run the risk of being put in a different division than you intend to compete in.
I have to qualify all of this by saying, I am not an RO and I haven't made this specific inquiry on the global village. I have however seen other inquiries about modifications that didn't provide any advantage in shooting, i.e. making your glock pink instead of black, and these modifications were not allowed in production division.