It seems somewhat easy to think of examples of ways to harm an agent without piercing its membrane, eg killing its family, isolating it, etc. The counter thought would be that there are different dimensions of the membrane that extend over parts of the world. For example part of my membranes extend over the things I care about, and things that affect my survival.
The question then becomes how to quantify these different membranes and in terms of interacting with other systems how they can be helpful to you without harming or disturbing these other membranes.
Aren’t existing research orgs already like this to some extent, where the organisation provides funding to its individual researchers in the form of a salary and they can form and run projects as they see fit? Or is this a naive understanding of how most research labs work?