My friends and I are playing through the Bespin Gambit campaign and decided to include the ISB Infiltrator side mission, since the rules in the blister pack allow for this.

The rules also state that it should be played as a forced mission. Am I still able to use agenda cards that can only be used during side missions?

Strictly no.

I made a similar mistake, buying an agenda card that could only be played on a side mission. The regular Bespin Gambit missions are story mission during that campaign, even when they are side missions otherwise.

Fortunately I was playing an extended Bespin Gambit with an added side mission, so I could still get to deploy Greedo... The mission didn't go that well, but ended up being pretty thematic.

You may ask the rebels if you can sell the card back. (Or let use it anyway.)