Can we require a 100% member vote to amend or repeal a covenant?
Yes, you can require 100% member vote to amend or repeal a covenant. While some statutes require a minimum number of membership votes to amend or repeal a covenant or by-law provision (for instance §339-(v)(j) of New York's Real Property Law provides that the by-laws may set forth "the percentage of unit owners, but not less than sixty-six and two-thirds percent in number and in common interest" required to modify or amend the by-laws), I am not aware of any statute which prohibits a maximum number required to do so.
I do not believe that it would be prudent to require the unanimous vote of all members to amend or repeal a covenant (unless your association consists of a limited number of members) since it would be difficult to obtain the consent of all members. While consensus among members is difficult enough to obtain, apathy alone could unrail an effort to obtain the requisite vote. Instead, I suggest that your association consider implementing a threshold somewhere between unanimity and a simple majority.