The eminent domain power is used to *permanently* acquire property; a compulsory license, as the name would suggest, is not a permanent taking. The compulsory licensing scheme set out in article 31 of the TRIPS agreement sets out a number of conditions that a country seeking such a license must meet, and the terms of the license are also limited in a number of ways (for example, the license "shall be authorized predominantly for the supply of the domestic market of the Member authorizing such use").
Importantly, if the conditions upon which the compulsory license is based (in this case, the inability for Merck and Brazil to see eye-to-eye on price) change, the license will *expire*. Thus, it's not accurate to imply that Brazil is acquiring the patent by what is basically its power of eminent domain. Brazil isn't acquiring anything really, since a change in circumstances could terminate its rights to continue using the patent.
And lastly, don't forget that (since this is a license, after all) TRIPS requires Brazil to pay Merck at some rate which will have to be determined later. Brazil wouldn't have to do that if it simply acquired the patent via its eminent domain power.
There is no royal road to geometry. -- Euclid