Sanders' line, "I do not have a super PAC, and I do not want a super PAC" is correct with the right terminology. He hasn't tacitly sanctioned a SuperPAC and there is no affiliation or coordination between the Nurses' one and his campaign. That's the difference, even though it's still an outside group contributing to the nomination/election of Sanders.
Not to mention most people inclined to support Sanders would see a very relevant difference between a superPAC funded by wealthy donors and one funded by a labor union. I mean come on.
I don't see why just because a special interest (which unions are) agrees with you makes it any less suspect, especially when your entire campaign is being run against "the corrupt campaign finance system."
It's a relevant point because Democratic primary voters are quite comfortable with unions and very uncomfortable with economic elites. Democrats do not believe that "Super PAC's" are terrible simply for philosophical reasons, they dislike Super PAC's because they're utilized by corporate interests, whether amenable to the Democratic Party or not. Further, the political action taken by, say, the SEIU pales in comparison with the tremendous amounts of money funneled into various PAC's and Democratic primary voters recognize this.