Someone's going to get upset, no matter what you do.
The people that are upset will be vocal about it. The happy people will keep quiet.
You can try to preempt resentment by consulting with the community. You can ask the community what they want, run polls, and keep the community informed the entire time.
Yet what the community wants and what's best for the community can conflict. The community doesn't know how to develop the community, they only know what they (personally) like. They don't see what you see. They don't have your data and expertise.
Sometimes they don't like (or don't use) what they've asked for (I've lost count of the number of exasperated community managers in this position).
Worse still, you can cause problems where non-existed. Say you run a poll; 33% of members vote for option A, 33% vote for option B, and 34% vote for option C. If you go with option C, that's 66% of the community that are unhappy.
Years ago I interviewed Jesse Cliff, co-creator of the online game Counter-Strike. He told me his secret. At every update, they would receive thousands of angry e-mails. They waited a few weeks to see which complaints were still coming and tracked user data to see the impact the change had made.
What can you do?
First, accept people will get upset. People don't like change. Don't get offended, just wait to see how things are after a few weeks. Track your data and see if usage goes up or down.
Second, let the community know what's happening and why. Don't ask if they would like a new site, tell a new site is coming and explain why. Keep them informed on the progress (most members wont be interested).
Third, let members have input within decisions. Members feel happier if they have had some input. So let them decide if they would like the navigation bar in red or blue, or if the text should be italicised or not. Just don't ask if they want a new site in the first place.
You need to force through some changes for the benefit of your community. Members wont always understand. They will resent it. By giving them information and some input you can alleviate some problems. Don't overreact to the negative reactions.