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If a Bloodletter attacks a Gaunt Summoner with Pug and rolls a six does it become a five and eliminate the mortal wound from the Bloodletters Decapitating Wound?

(Pug: Your opponent must subtract 1 from any hit rolls that target the Gaunt Summoner in the combat phase, as long as he is accompanied by Pug)

We came across this yesterday. My opponent thought that rules which change hit rolls affected the target number and not the die roll itself.

This is something that many people ask about in AoS as it works alittle different than many other games. The answer is that you subtract 1 from the roll, so a roll of 6 becomes a roll of 5, and therefor does not cause any mortal wounds.
On the other side, if you find an ability that lets you add 1 to dice roll, each roll of 5 becomes a 6 and will cause mortal wounds as well

Edit: This is also why most such abilities read "if you roll 6 or more", because you can add to the roll.

Yup. Though note a 20+ man unit of bloodletters will be getting a bonus which cancels.it out.