You can use SatisfiabilityInstances to get them as follows
gg = GridGraph[{2, 3}];
edge2clause[e_] := ! (e[[1]] && e[[2]]);
clauses = edge2clause /@ EdgeList[gg];
formula = And @@ clauses;
vars = VertexList[gg];
instances = SatisfiabilityInstances[formula, vars, 1000];
independentSets = Extract[vars, Position[#, True]] & /@ instances
Notebook
Good idea. Thank you for sharing with us.
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