I'm not the biggest fan of the facility that the university at which I work provides for me to lock my bike, but I use it because even though I have several places on the floor where I work that I could store the bike, it would upset some people. Even though several thousand people walk past my bike every day, I've never had an issue, even when leaving my lights and bags on the bike.

When my bike was new I didn't want to let it out of my sight. If I was riding a $4000 wunderbike, I wouldn't want it out of my sight, so I understand your desire for some sense of security, but company policy is company policy. Either follow that policy or find another company. Alternatively, a beater bike, a Craigslist special, can be found for $200, even around here. I wouldn't ride a bike to work, or in a major city for that matter, that would cause me significant hardship if I lost.

The worst situations arise from simple misunderstandings and grow because of poor communication. Maybe the fellow who reported you had been written up for something last week, maybe he is the shop safety officer, maybe he had a bug up his butt, but whatever the reason, he is right according to the company policy and you are wrong. If called to the carpet, explain why you were using the room to store your bike and talk about the potential inadequacies of the existing bike facility. Maybe some good can come of the situation, but it's more important to have the job (unless you have a trust fund you're not telling us about) than it is to fight this battle.