Answer: Since guineas can fly, you are correct in that the only way to contain them is to pen them up. They are probably doing some good in your garden in that they do eat insects and are a source of free fertilizer, and since they don't scratch for their food, the guineas do less damage than hens would. That is small solace, I know. I'm sorry I don't have a solution for you, except to suggest that a fence around your flower beds might be enough of a deterrent to keep them out if they have sufficient roaming room and a good source of food and water elsewhere.
One other possibility--I've seen people keep seagulls out of their swimming pools by stringing fishing line over the pool. Several strands placed a few feet apart from 6-foot tall poles may confuse the birds so they won't land in the garden. And a short fence might just keep them from walking in.
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