Thomas Jefferson asked Congress to suspend the privilege of the writ of habeas corpus in connection with Aaron Burr's actions. IIRC, the Senate gave its consent but the House did not, so habeas corpus was allowed. That seems ample precedent for Lincoln to ask Congress for a suspension rather than assume the duties of the legislature himself.
Then there was the case of General Andrew Jackson who suspended the writ and even jailed the judge in 1815 following his victory in the Battle of New Orleans. The following used to be on a DOJ web site, but my old link to it no longer works.
Major General Andrew Jackson Indicted
A very interesting case occurred during the tenure of United States Attorney John Dick in 1815. Just after the Battle of New Orleans during the War of 1812, United States Attorney Dick indicted Major General Andrew Jackson on charges of obstruction of justice. Jackson also was charged with contempt of court. According to the indictment, Jackson had "...disrespectfully wrested from the clerk an original order of the honorable the judge of this court, for the issuing of a writ of habeas corpus in the case of a certain Louis Louallier, then imprisoned by the said Major General Andrew Jackson." Jackson incurred the charges of obstruction when he imprisoned the judge who had charged him with contempt. When the future President of the United States appeared in court, he refused to answer the interrogatories and promptly received a fine of $1,000 which he paid and then left the court. Leaving the courthouse, Jackson stopped and spoke to a large crowd that had gathered:
I have during the invasion (of New Orleans) exerted every one of my faculties for the defense and preservation of the Constitution and the laws. On this day I have been called upon to submit to their operations, under circumstances which many persons might have thought sufficient to justify resistance Considering obedience to the laws, even when we think them unjustly applied, is the first duty of the citizen, and I do not hesitate to comply with the sentence you have heard pronounced; and I entreat you to remember the example I have given you of respectful submission to the administration of justice. (As quoted in Proceedings of the Louisiana Bar Association, 1898-1899, p. 120.)
That is precedent for Lincoln on what to do if you suspend the writ without the approval of Congress.
Let's see if I understand this -- general & future president Andrew Jackson first suspended habeas corpus, then later, after the crisis had passed, apologized and paid a fine for it?
By contrast, Congress debated President Lincoln's actions at great length, and in the end decided to neither censure nor indemnify him for them, but to grant him Congressional authorization to suspend habeas corpus.
Seems to me, that should settle the question.