Its a portion of Itachi's powers. And its a last resort option, because Itachi doesn't want Naruto to use it. So maybe its lethal to the user?
1. Just as you said, it could be something dangerous (to naruto or who ever he's using it against).
2. The statement was made implying that certain events (ex: Sasuke attacking konoha, joining madra, war ,etc.) don't transpire.
A lot of people take the statement Itachi made is due to him giving Naruto a power or jutsu that will harm him or Sasuke. I think the statement was more indirect than direct. The reason is because we don’t know if the power he gave Nauto is something that will help Sasuke (like a flashback of what really happened at the Uchia Massacre). If this is the case then Itachi would be implying that he hoped Sasuke took a different path rather than join Madara and due to the thought of Sasuke joining Madara and attacking the village that’s why he made the statement. “I HOPE THE DAY NEVER COMES WHEN YOU HAVE TO USE IT” he didn't say it because he gave Naruto his power, but for Sasuke not making the wrong decesion that will lead to the day Naruto will have to use it. This may be confusing to some, but this is just an opinion.
I very highly doubt Itachi gave Naruto something that would be lethal to him if he used it. That would just be silly on Itachi's part. As we know, Itachi thinks a million bajillion moves ahead in life (might be a slight exaggeration), so at the very least, he certainly thought there would be a possibility that his "gift" might not work. So he definitely wouldn't have made it lethal to Naruto.
Your interpretation of Itachi's line is just a around about way of saying Itachi hopes Naruto won't have to use it against Sasuke. That and Itachi outlined most of that when he was talking to Naruto just before he gave him some of his power (What if Sasuke attacks the village? What will you do?). Everybody else just jumped to the natural conclusion that other stuff is obvious.
Theory over, Shisui's eye it was.