In terms of rights, you may be limited by privacy requirements on those staff/executive portraits. Make sure to have a model release form signed by the subjects you want to use for promotional purposes. Remember that they may not want to have their photo displayed elsewhere.
The model release form should allow the subject to choose where their photo is used. Perhaps if you have a check box to opt out of personal promotional use (apart from being on the company website).
I'd say you would absolutely benefit from taking a professional approach to the photography (contracts, licensing, pay) from the start. Your software developer role likely doesn't include photography so that's probably why they're offering to pay, since they would otherwise pay another photographer to do it.
Nice work on the site's photography too!