Safe way of riding has the most of the ecological impact. If you hit even not a human, or just have near pass somebody has seen, this promotes the view that bicycles are not safe enough for practical use. This may prevent somebody from switching into this way of transportation.
Due that I think it is better to use say lights in the night, even if they have ecological impact. If I ram into something in the midnight with no lights, somebody will say "what an idiots these cyclists are". This discourages others from using bicycle for commuting.
For the same reason, I think, disk brakes are more environmentally friendly, as they give more control on the bicycle, this way reduces the number of accidents, this way increases the popularity of cycling. I have disk brakes on one bicycle and rim brakes on another and when I switch the bicycles I clearly see the difference. This way no brakes at all (I mean, a fixie) will do more ecological damage if you get into accident preventable by having a brake.
If you can maintain the rim brakes so that they are equally efficient, this answer does not apply to you.