I'm a bit late to the party but wanted to share my experiences. I'm right in the middle of a similar situation at the moment. My partner is from a different country (I'm from the UK) and our visa options to continue living together in the UK ran out before we had time to properly plan a wedding. We are planning a July 2017 wedding but two weeks ago I flew to his home country (in South America) and did the registry office thing with some of his mum's acquaintances as witnesses. My partner's parents were there, and as his family are huge and very excitable we couldn't stop a small cohort of them attending too, so we ended up with a party of about 12. We went to the botanic garden and had a nice meal after. The day after the certificate translation came through, my partner applied at the nearest British Consulate and he should be back in the UK with me in 3-4 weeks, if all goes well (HOORAY).
The lessons I've learnt so far include: (1) keeping the secret is DIFFICULT. I've been wracked with feelings of guilt at times. Also logistically people inevitably will find out. My plan was to say "we got engaged and signed some papers to help with his visa" to all but very close family. But I explained the full story to anyone who has asked, and spontaneously to a few people as it's hard to hold such a huge thing inside when you're talking to close friends. So lots of people know now. I would be concerned as to how it would impact my "proper" wedding next year, if it weren't for the fact that almost everyone has been extremely vocally understanding and supportive. (2) Be prepared for your personal emotional fallout. I was extremely blindsided by how crazy emotional and significant even the tiny municipal foreign registry office thing was for me. I really LOVE this guy and now I have a legal document allowing me to be with him, anywhere, forever?! This is a BIG DEAL and there's pretty much nothing that can reduce that. These happy emotions, however, led to more feelings of guilt - the feeling that "I've had my happy time" and would be greedy to want more. You should be prepared for these feelings, but also know that they are silly, and lead directly on to point number (3): that you don't need to feel guilty or ashamed, and don't let yourself or anyone else let you feel that way. Much of the rigmarole of weddings are socially constructed, but they are really just about two people and two families coming together, sharing their love, bringing some net happiness into the world. You don't need to fulfil all the imaginary etiquette to make these core things happen. Some people have showers and bachelorettes and engagement parties, some don't. Some do the wedding and legal stuff on the same day, many don't. The world isn't perfect and in some cases, tragic or difficult circumstances get in the way of what you personally envisioned for your future. I disagree that you need to shy away from the terminology "wedding" for your second event, to be honest. A wedding is, if nothing else, a celebration of love and commitment made in front of family and friends, and this is exactly what you will be doing. This is your thing, you do you, and don't let others who aren't living your situation make you feel bad for it.
Some more practical advice would be to keep important things for the second event: we didn't exchange wedding bands, read vows to each other, I haven't changed my name, obviously none of my family or friends attended at all and we didn't do any of the big reception/dances/speeches things. All these and more will help to conceptualise the two events as seperate. And finally make sure sure that everyone involved is on the same page emotionally and practically - this can be hard and delicate and draining, but if they are close loved ones they should be able to understand your way of thinking. Anyway, good luck with your wedding and your future!
(Apologies for formatting, am on mobile; and for wall of text, am just verbose.)