I found this (below) on a "wisegeek" site. Carrageenan is very much like agar chemically -- so I can't see why it would be a problem -- as long as you avoid carrageenan processed for industrial use.
Health Concerns (from wisegeek):
Several studies in the early 2000s suggested that a certain type of carrageenan — degraded carrageenan, which has been hydrolyzed, or broken down by acid — could cause gastrointestinal problems, including cancers. The degraded type is not typically used in food. In fact, only the undegraded variety has been deemed safe for human consumption by the Joint Expert Committee on Food Additives (JECFA) and approved for use in foods by the Food and Drug Administration in the US.
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