Just to show that the JIF isn't everything, PeerJ is one of my favorite journals, for reasons many of which appear here. There are other respectable journals that don’t yet have a JIF. Examples include Tremor and Other Hyperkinetic Movements (too new for a JIF, but edited by Elan Louis, a movement disorders neurologist at Columbia University, and has published some good Tourette papers). Another favorite of mine is F1000Research, which also explicitly rejects the JIF, as it works to publish any sound research contribution.
Whatever journal you choose (except for some holdouts like Am J PsychiatryNeurology, and Lancet titles), you can send a preprint to bioRxiv or PeerJ Preprints before you send the manuscript for publication. That protects your rights substantially. Even for journals that usually do not allow preprints, you can email the publisher in advance to check whether they'll allow it (for instance, some Cell Press titles do not explicity allow preprints but say, "you can ask").
You can also submit a SPARC addendum to the journal’s copyright transfer form (http://www.sparc.arl.org/resources/authors/addendum) and see if the publisher accepts it. That’s what I did with my last paper for my society journal, the Journal of Neuropsychiatry and Clinical Neurosciences (https://www.ncbi.nlm.nih.gov/pubmed/28121259/#comments).