The terms of the new deal between the Guinness Premiership clubs and the RFU state that players in England's 32-man squad must be rested for one of the games between rounds nine and eleven of the Premiership.
"Next week, I've got to take Borthwick out," said Jones, whose Sarries side overcame league leaders London Irish at Vicarage Road on Saturday.
"To me that is ridiculous. I'd rather take him out of a European Challenge Cup game and he wants to be out of the Challenge Cup game.
"Why have an EPS squad that takes your best players out of the Premiership?"
The new EPS agreement had been anticipated to make the relationship between the English club and international game a smoother one but Jones believes this particular rule isn't helping either party.
"We should be having our best players playing every game," explained Jones.
"It's just crazy. He's (Borthwick) got to sit on the sidelines next week and twiddle his thumbs.
"He could sit and do that against Mont de Marsan (Saracens' pool opponents in the European Challenge Cup on January 23), have a nice coffee and croissant and watch the boys win by 30 points.
"Why leave him out against Gloucester, when you could pit him against Alex Brown and see how good Alex Brown is? It's crazy.
"It should be about the welfare of the players. Borthwick needs a week off before the Six Nations so what's sensible for him? Viadana at home or Mont de Marsan two weeks before the Six Nations.
"Is it going to be good for his rugby to miss Gloucester next week? No way. There have got to be better ways to do it."