Recently, I was asked about some resources on Cromwell and Owen. Here is a rough bibliography. This is not meant to be exhaustive, so please feel free to add your two cents!
On the subject of conscience and authority in relationship to Cromwell:
If you have access to dissertations, Sarah G. Cook's "A Political Biography of a Religious Independent: John Owen, 1616-1683" (PhD, Harvard, 1972) and Llyod G. Williams's "Digitus Dei: God and Nation in the Thought of John Owen: A Study in English Puritanism and Nonconformity, 1653-1863" (PhD, Drew, 1981) are good places to start.
On Cromwell: Unfortunately, I've yet to get my hands on Martyn Bennett's new work, so no comment. Antonia Fraser's classic Cromwell provides good background info with scattered references to Owen. Peter Gaunt's Oliver Cromwell regrettably makes no mention of Owen, although it is a standard. His annotated bibliography is helpful. Likewise, Owen receives minimal attention in John Morrill's Oliver Cromwell and the English Revolution, but this work is a landmark study on reassessing Cromwell. I should also mention the forthcoming OUP title by Crawford Gribben, God's Irishman: Theological Debates in Cromwellian Ireland. Haven't seen it, but I'm looking forward to it!
Perhaps the most useful resources for this topic are the works by Barry Coward, Maurice Ashley, and Christopher Hill. Coward's Cromwell (ch. 7, esp. 152ff) and The Cromwellian Protectorate (ch. 5, esp. 110ff) argue that Owen “played an important role in weakening their commitment to the Protectorate by awakening their consciences to the dangers of pride and ambition.” Although dated, Ashley makes a similar point in Oliver Cromwell and the Puritan Revolution and The Greatness of Oliver Cromwell (cf. p. 364). He states, "liberty of conscience was the main cause of the civil wars and its security the leading purpose of government." Hill's God's Englishman (ch. on King?) and especially his The Experience of Defeat (170, passim) deal somewhat extensively with Owen. In the same Hillian vein, see also Ivan Roots, "The Tactics of Commenwealthsmen in Richard Cromwell's Parliament," in Puritans and Revolutionaries, eds. D. Pennington and K. Thomas.
On the subject of conscience and toleration (esp in relation to Locke):
The place to begin is Paul Lim's recent essay, "The Trinity, Adiaphora, Ecclesiology, and Reformation: John Owen's Theory of Religious Toleration in Context," WTJ 67 (2005): 281-300. This is a must read. See my notes on this article. C. E. Whiting's Studies on English Puritanism from the Restoration to the Revolution, 1660-1688 is an oldie but a goodie. More up to date, Gary S. De Krey has some helpful comments on Owen in his "Reformation in the Restoration Crisis, 1679-1683," in Religion, Literature, and Politics in Post-Reformation England, 1540-1688, eds. Donna B. Hamilton and Richard Strier and especially Wayne J. Baker, "Church, State, and Toleration: John Locke and Calvin's Heirs in England, 1644-1689" in Later Calvinism, ed. W. Fred Graham.
The best one volume text on the history of the Restoration—with passing mention of Owen's contribution on toleration—is without question Neil H. Keeble’s The Restoration. Other pertinent texts include John Spurr's English Puritanism, 1603-1689; idem, "From Puritanism to Dissent, 1660-1700" in The Culture of English Puritanism, 1560-1700, eds. C. Durston and J. Eales; and O. P. Grell, J. I. Israel, and N. Tyache (eds), From Puritanism to Toleration.
