With the upcoming SLiM, mutations won't have metadata; the equivalent information will go in top-level metadata. So, msprime should just not add metadata to the mutations; and pyslim will have a method that puts appropriate things in top-level metadata. Note that the only piece of actual information that msprime puts into metadata is the SLiM time, which is just a simple transform of the mutation time anyhow, so no information is lost.
With the upcoming SLiM, mutations won't have metadata; the equivalent information will go in top-level metadata. So, msprime should just not add metadata to the mutations; and pyslim will have a method that puts appropriate things in top-level metadata. Note that the only piece of actual information that msprime puts into metadata is the SLiM time, which is just a simple transform of the mutation time anyhow, so no information is lost.