Is using CFL bulbs without a ceiling covering them bad?
When you say "ceiling" I take it to mean a fixture lens or diffuser. All fluorescent lamps put out light at a high frequency that can be bothersome to some people. This frequency is determined by the ballast, which will vary by manufacturer and lamp type. The actual shape of the fluorescent tube makes little difference in the frequency unless the ballast is changed as well.

Diffusers and reflectors tend to mask the high speed off/on effect that is bothersome. Directly seeing the bare tube will more likely be bothersome than any other configuration. You've also dramatically changed the light dispersal pattern of the fixture by using CFLs in place of the intended halogens. This could also be why the new configuration is making you uncomfortable. Another factor could be the CFLs are putting out more light than the halogens did, amplifying the effects from other factors.

You might consider LED lamps that come in smaller packaging and may more closely replicate the dispersal pattern achieved by the original halogens. If you want to stick with CFLs, consider using those where the tube is encapsulated by an integral diffuser.