It would do not good to prohibit agencies from testifying before Congress. As long as the Congressional committees control the agencies' budgets, the agencies will have to listen to what they say -- not testifying would make no difference to that relationship.
One thing I can think of would be to stop having the most interested committee oversee the agency and its budget. In other words, the Ag Committee, made up of farm state members, would need to stop overseeing the Ag Department. Then the members of the committee that oversaw the USDA would not be so interested in trying to control them.
But this really strikes me as being pretty antidemocratic -- to prevent the people most affected by agriculture from having control of the Department of Agriculture. I think the only real way would be to have countervailing pressures from other interest groups. We would have to form interest groups that were opposed to what the iron triangles want.
For example, if the agriculture iron triangle wants wasteful farm subsidies, we would need to have an interest group that would work hard to lobby against those subsidies. This would be the only really effective way of breaking iron triangles -- to have different interest groups lobbying the way that pluralist political theory says they should.