If you look at the xml file you'll see in the table definitions at the top that "false" is the default value for the "ResearchAgreementTradingAllowed" column. Either deleting the line in the Philosophy entry or changing its value to "false" will accomplish the same thing and carries none of the risk you suggest. All the xml files are used for in this game is to load values into database tables. This is explained in the modding guide. If doing this before a new game doesn't disable research agreements it may be a caching issue.