Sentence:  The President ... was of opinion, that the arming and equipping vessels in the ports of the United States to cruise against nations with whom they are at peace, was incompatible with the territorial sovereignty of the United States; that it made them instrumental to the annoyance of those nations, and thereby tended to <WSD>compromit</WSD> their peace ... 
Meaning of the word marked with <WSD> tags:  To compromise.