There are a few ways going about this, but they all include being up-front with the users and maybe taking some heat for it. After all, any change breaks someone's workflow.
Ask for Suggestions
"How can we improve this design?", "What is your opinion on this?", "How is this compared to X?".
Asking for suggestions and encouraging meta-discussion is a great way for members to show what they want and how the change can be improved or made easier to cope with. It also helps show the users that the moderators care about the user's opinions. Giving a sneak preview might also be helpful as it shows what to expect.
Give a Grace Period
Note: You shouldn't do this if keeping the feature opens you up to potential exploits of your system.
If the change doesn't need to be implemented right away, you can make an announcement wherever saying that certain functionality might be changed with a rationale and a shorter message (maybe even linking to the announcement) when attempting to use the feature (if it can work).
Add A Different Requested Feature
If the users has a feature that they have wanting for a long time and the circumstances allow, add a feature that your users have been requesting. Especially if the overall response is negative, take the time to add that feature that is wanted if it is possible.
Be Prepared To Take Heat
Most people that speak up about the changes are against it, and some vigilantly so. Be prepared to take some heat for it, and in some cases, a lot of heat. Some changes anger the vast majority (or a vocal minority) of users and some may stop at almost nothing to get their feature back or leave the community.