Bernie Sanders has strong beliefs and believes in fighting for them. He might be willing to accept that Hillary Clinton is the candidate he will be voting for, but he has not giving up on making this country the way he wants it to be. That includes calling out things that he believes are wrong.
It is my belief that Hillary Clinton and Bernie Sanders are just too far apart on too many issues to expect that Bernie will ever even remotely end up supporting Hillary in any way despite their shared party. He will continue to be, as the question asks, a thorn in her side.
Like the proverbial gadfly, Bernie Sanders is causing the Democratic establish to examine their position on the TPP. Sanders feels the TPP trade deal is unfair to U.S. workers. , Clinton has already changed her position on this deal, but many of Clinton's allies have not embraced Sanders position, so it is likely that Sanders will continue to advocate against the TPP.
Yes, Bernie Sanders will continue to be a thorn in Hillary Clinton's side. Being a part of the same political party is not enough to bring the two together in harmony. Unfortunately, Sanders has not seen fit to begin unifying the Democratic party and continues to work against Clinton as if he is still on the stump. Sanders needs to find a middle ground and use it to propel the party forward.