If something is bad, then it's bad even when it's done by your team.
The end does not justify the means.
Corporations are not just businesses. They are the way that people with a common interest can pool their resources to coordinate on a common goal.
The fix doesn't lie, however, in hoping that businesses will voluntarily stop lobbying, so I won't criticize back-country tourism companies from giving money to the Sierra Club to ensure that their venues remain unspoilt. Even if a business didn't want to, it might nonetheless feel compelled to lobby congress for reasons of competitive advantage. When many entities feel compelled to act in opposition to their ethics, it's a sure sign that the system they operate in is broken.
(That said, many businesses sponsor the Sierra Club for P.R. reasons, which is fine and categorically different from the "bad lobbying" explained above)