It was kind of game over once the search warrant for key came in, unless the keys were in an HSM. As long as you can prevent the search warrant from being issued, a regular pen register isn't going to be terribly onerous if it doesn't produce useful data due to everything being encrypted. If you don't have a system to do user logging, you can honestly respond "we do not have records of messages sent through our system". I don't know if they can even require you to turn logging on if it's not already on in that case; they could get a warrant for your whole system, possibly, but that's a much higher legal bar, and "fine, it's in fedex billed to USG account" might be a reasonable answer there.
(IANAL)
I assumed this stuff only applied to CALEA entities like PSTN, PSTN-interconnected-voip, and broadband ISPs; it appears it is actually patriot and means there's enough legal pretext to essentially always get keys:
1) Any non-CALEA entity probably does NOT have a system which can log every pen trap piece of data desired. If there's even a single thing which your system internally can't provide, LEA could argue that their own pen trap would be more effective, and could compel you to turn over keys to populate their device. They could compel you to generate new keys outside an HSM if you have technical controls to protect your existing keys from disclosure, too, and disguise that as "hsm failure" or something like that. It seems pretty open ended.
A non-charitable view of the entire Lavabit thing is that it was a roundabout way/pretext to compel key disclosure. It doesn't matter if USG uses the keys illegally for something which isn't used in a criminal prosecution; the data in Snowden's mail is of intelligence value where those rules don't apply.
2) Unless Patriot 216 is found unconstitutional, Ladar is fucked, as is the entire US IT/cloud industry. I don't believe in Lavabit's "keys are protected" argument -- the court presumes LEAs are trustworthy, and will accept just restrictions in policy on what they can do with keys. Only eliminating pen registers for "arbitrary Internet services" will work, and that probably won't happen.
(IANAL)
No, in fact, when dealing with law enforcement you should be as uncooperative as possible. It is in your best interest. The expectation that if we are polite to some adversarial authority then they'll go easier on us seems quite widespread (seems to me it has some deep bio/psychological roots). Unfortunately, it's completely false. The police doesn't care the least bit if you are cooperative, polite, prompt, not a dick... In fact, they are trained to exploit one's urge to be polite, honest and helpful against you.
If law enforcement decides to come after you (for whatever reason), no politeness in the world is going to make them turn around and say: "Gee, what a nice fellow, we're sure sorry we wasted his time." They are there to get you, not to negotiate and make good first impressions. There is absolutely nothing you can say that can help you in any way.
The classic: https://www.youtube.com/watch?v=K1p3K3sC1Ec
Some companies probably just rolled over and agreed costs directly with the agencies involved.
That sounds almost like a solicitation for work, and I suspect that is the way that others (Google, MS, friendface, et al) replied.