IGNORE WHAT'S BELOW. IT'S INCORRECT.

Well, IANAL, but, I believe, technically, such modifications still have to be under GPL-compatible license (or organization is violating original authors' rights). I.e. anyone within the organization, who had used the software, must be granted all the freedoms GPL requires to be granted. Whenever organization members actually exercise those rights are up to them, of course.

I don't think it's a bad thing. It's only fair - if your business relies on proprietary sauce that you really want to keep secret - some may still consider helping you (and they use BSD, MIT or LGPL) while some may not want it this way (and use GPL or AGPL).

I've updated the comment.

1. Employee executes GPL binary on company's computer. I'd consider this binary to belong to owner of the computer - the company. So employee may not have the right to ask for the code.

2. Employee gets GPL binary from company, executes it in his computer. Is he forbidden to get access and distribute the source code? Can a company make restrictions around the GPL to its workers?