I'm not sure I follow what you're getting at.
Yes, Ned knows Jon's lineage, his sister asked him to keep Jon a secret because if Robert found out, he'd kill Jon. As he was a Targareyn and well, she kind of cheated on Robert with Rhaegar and Jon is the result, so yeah, Robert would rightly be pissed and kill Jon. So, Ned was protecting Jon before he found out about Gendry. Gendry's lineage is irrelevant when it comes to Jon.
Ned sent Gendry away from King's Landing because Cersei was killing all of Robert's ******* offspring, as those children might have had a claim to the throne, more so than any of Cersei's kids because they're not in line for the throne seeing as how they're incestual offspring of Jamie and Cersei.
So, no, I don't think Ned was using Gendry as cover for Jon. He was keeping Gendry a secret just like Jon.