In 2020, we initiated a systematic study of graph classes in which the treewidth can only be large due to the presence of a large clique, which we call $(\mathrm{tw},ω)$-bounded. While $(\mathrm{tw},ω)$-bounded graph classes are known to enjoy some good algorithmic properties related to clique and coloring problems, it is an interesting open problem whether $(\mathrm{tw},ω)$-boundedness also has useful algorithmic implications for problems related to independent sets. We provide a partial answer to this question by means of a new min-max graph invariant related to tree decompositions. We define the independence number of a tree decomposition $\mathcal{T}$ of a graph as the maximum independence number over all subgraphs of $G$ induced by some bag of $\mathcal{T}$. The tree-independence number of a graph $G$ is then defined as the minimum independence number over all tree decompositions of $G$. Generalizing a result on chordal graphs due to Cameron and Hell from 2006, we show that if a graph is given together with a tree decomposition with bounded independence number, then the Maximum Weight Independent Packing problem can be solved in polynomial time. Applications of our general algorithmic result to specific graph classes will be given in the third paper of the series [Dallard, Milanič, and Štorgel, Treewidth versus clique number. III. Tree-independence number of graphs with a forbidden structure].