this is particular area of interest from me. I came from a Yogic background to Buddhism and noticed a lot of similarities but that the teachings on the chakras were missing... my personal opinion is that the Buddha was concerned primarily with liberation and teaching on & manipulation of the chakras isn't part of that path
necessarily.
the chakras are part of the body, and should be treated as such re: mindfulness of the body. worrying about you or anything else effecting your chakras is about as useful as worrying about catching a cold. the conscious control of an untrained person over their energy system is about as much as over your heart... nearly nothing. the idea that you may have opened, or unbalanced a chakra is strictly a product of new age bastardization & isnt (to my knowledge) found in the traditional teachings.
that being said I've found the practices extremely useful in general, as well as with my current practice. Yoga & Qigong are the most refined, and imo best, systems to study if you can find a legitimate teacher (which is hard). There are Buddhist teachers as well who teach about somatic energies and their usage, re: Thanissaro Bhikkhu, Ajahn Lee Dhammadharo, & Ajahn Succito They have, again imo, a much more practical and useful teaching on the subject than you will find otherwise.
Worrying that a thought may or negative feeling will 'infect' you is pointless. Intrusive or negative thoughts, in my experience, are much more effectively dealt with the methods taught in MN20 Vitakkasanthana Sutta:
http://www.accesstoinsight.org/lib/auth ... el021.html.
“The unawakened mind tends to make war against the way things are. To follow a path with heart, we must understand the whole process of making war within ourselves and without, how it begins and how it ends."