1. Which places could the issue of an individual member of an NGO violating UN rules (with the potential consequences of striking off the NGO in its entirety) be raised and dealt with in the process/agenda for the meeting of the COP? What would be the decision making – voting rules/consensus required etc?
2. How would above work legally and procedurally and in the context of the current accreditation process? Are the two incompatible?
It is our impression that ECOSOC-resolution 1996/31 (consultative relationships UN-NGOs) does not apply here since we’re not dealing with an actual UN body, but rather with a Treaty body.
Article 7(6) UNFCCC as well as relevant secondary instruments (Art. 7 RoP (FCCC/CP/1996/2) and decision18/CP.4), which do apply, all state that NGOs may be admitted unless one third of the Parties object. Absent more specific rules, it appears from this that an NGO can be deprived of its observer status if 1/3 of the Parties so decide, irrespective of the precise reasons for this (i.e. not only under the conditions of ECOSOC-resolution 1996/31).
Disrespect of Member States’ flags is explicitly prohibited in the Guidelines for NGO-participation in section B.4: “The flags and any officially recognized symbols of the United Nations and of its member States shall not be treated with disrespect.” 
An alternative (and less radical) option is provided in the UN Security guidelines related to media actions, distribution of publicity materials, and use of UN emblem at UNFCCC Conferences. This document a.o. prohibits action derisory to the UN or any of their Member States that would go against basic rules of decorum.
Possible sanctions (in both cases) include confiscation of a representative’s accreditation badge or removal of a representative from UN premises. These sanctions can be applied by the secretariat and by UN Security without any political decision.
In our view, the issue could be raised both as an SBI Art. 6 agenda item and as an accreditation agenda item.