Hellsing Team is pretty hardcore, they have much more durability than the Naruto Team, and they even regenerate. Depending on which Naruto and Kakashi are participating this could go either way. Current Naruto and Mangekyo Kakashi are pretty hardcore as well, Minato is fast as hell, and Sarutobi haves a lot of firepower, so does Jiraiya. In other conditions I'll side with Naruto Team if the characters are at their top shape, but if Naruto is base shippuden level, Hellsing team haves greater chances.
But using the conditions listed above, Hellsing team haves some edge since Minato and Sarutobi doesnt know that they need to seal their opponents, and they dont know that they are almost inmortals. And if they are in character the guys from Hellsing are ruthless killers while Naruto guys have to get pretty pissed off to kill (At least Naruto needs to be pretty damn angry to use his full power)
I think this maybe be very tough .
Team Naruto as the speed advantage with Minato being hyper-sonic and said several times to be the fastest in his universe through his technique of the Flying Thunder God .Naruto being implied to be as fast makes him the second hyper-sonic of the team in his Chakra mode. Jiraiya kee ping up with Pain should put him in the supersonic range at lowest.
Hellsing has Anderson who sliced Alucard's arm off before he could of reacted when the later could react to a Mach 2.8 bullet.The Captain kept up with Seras.Who dodges bullets after they were fired .Alucard is basically the one who "fathered " Seras.The whole team is supersonic
Speed goes to Naruto
Naruto fires the Rasenshuriken which causes city-block level damage,the tailed beast bomb(if the Kyuubi decides to obey him).Kamui,the seals of Minato and Sarutobi bypass the durability of the team.
There is seemingly no 'perfect' way to truly say goodbye. So I gathered a bunch of them!