When he was mayor of New York City, Michael Bloomberg proposed a ban on any "sweet drinks" more than 16 ounces. Although it was ruled illegal by the courts, other cities (notably Mexico City) have started to introduce this kind of legislation. The new mayor of New York, Bill Di Blasio, is thinking about reintroducing this proposal. Is this an intrusion into personal freedoms? How should suppliers of these products react?

Clearly, a ban on these drinks would intrude on personal freedom.  The issue is not whether it intrudes on personal freedom but whether it does so excessively.
Essentially every government law infringes on personal freedom in some way.  The speed limit intrudes on our freedom to drive whatever speed we want.  The ban on cocaine and heroin infringes on our freedom to do whatever we think will make us feel good.  The ban on sugary drinks would infringe on our right to eat and drink what we want.  However, while laws always infringe on our freedoms, we accept them because we think they do not intrude too much in comparison to the bad things that they prevent.
It is in this context that we have to think about the proposed NYC ban.  Does it do enough good to overcome the way in which it infringes on our freedom?  A ban would presumably help at least somewhat to reduce the problems associated with obesity in the city.  This would make people healthier and reduce the government’s need to spend on health care.  The question you have to answer for yourself, then, is whether that is enough of a benefit to justify telling people what they can and cannot drink.  One thing to think about as you consider this question: where do we draw the line?  Could the government ban us from eating large steaks (or all meat) because it thinks fat is unhealthy?  This is a matter of personal opinion.  What do you think?
As for what companies should do about this, I would say they should do two things.  First, they should advertise, telling people to fight for their right to eat and drink what they want.  Second, they should work to develop new drinks that would have less sugar. If they could do that, they would be covered in the event that such a ban does eventually end up happening.
https://www.huffpost.com/life/topic/soda