Well, maybe I'm not smart enough or I misunderstood some really basic concepts, so please let me make this clear:
1) Naruto got hit by a jutsu that feeds off whenever he USES chakra (never mind molding chakra or natural way his body creates chakra, just when he uses it on a technique).
2) That plant also feeds off Kyuubi's chakra, but only when he pushes it into Naruto.
3) The plant has 5 stages and right now is in stage 3, plus being irremovable, by changing Naruto's body cells, muscles, tissue and bones.
Sure, that jutsu sounds powerful - for a normal ninja. But we're talking about Naruto here, two years after the war. His chakra reserves were Jounin-like during his Genin time already and when combined with Kyuubi, it was on par with the deadliest and most powerful ninjas in the whole world. Why didn't he use all of that chakra to overfeed the plant or simply burn it away from his body? Sure, it would hurt like hell, but his healing factor preserved him from direct stabs all over his body including heart. Or he could ask Hinata, Neji or any Byakugan user for help. Their ability to see chakra and cut through it like butter, including tenketsu and chakra circulatory system, could sever that plant from Naruto's body or at least damage it over time to make it drop off. Why didn't Sasuke or Sakura think of that?
Even if that would be impossible, Naruto could still do one more thing, exactly what he did against Pein's Preta Path - his senjutsu. Natural energy is impossible to control by anyone without master or grandmaster chakra control (something I doubt a mere jutsu could have) and would turn that plant into a stone in a matter of seconds. I guess that wouldn't be too comfortable either, but it would definitely stop it and allowed for its removal safely. I know Naruto is baka here, even bigger than in the manga, but at least Sakura or Hinata could think of that (both of them saw his fight against Pein).
To move a little bit from Naruto, I didn't completely catch Sasuke's fight before, but did he really got caught up in genjutsu? Sasuke, on par with Naruto, with Sharingan that is able to break through most (any) genjutsu? Did he lost his touch in the last two years or did he do it deliberately to test his opponent? If it's the latter, then it severely backfired.
I'm not trying to make this doujin look bad, I just found it today and enjoyed most of its parts (some of them more or less realistic than others), but in the matter of powers, it looks mostly like Naruto is being quite a pussy here and Sasuke, despite all of his cool look, didn't fare any better. Ironically, the strongest of Konoha's shinobi so far are Sai, Karin and Sakura. I like them strong and dependable, but should we switch Naruto for a doll, it wouldn't change any impact he had on the story so far.