Restricting user freedom of customisation

The context:

Currently working on the redesign of an employee attendance app that's used by various companies. At the moment the companies that use the app can set their own attendance statuses to fit their needs.

For example Company X created and use the attendance statuses: Present, Late, Absent. Whilst Company Y uses: Present, Absent, Absent without notice.

We give the client companies full control over how many and what options of attendance they want to use so it differs from company to company.

Now this is all fine and dandy until you look at the user interface (I'm not obliged to show you and it doesn't hold relevance anyway since the redesign is well underway) which is a complete mess as you have to cater for so many possible options and it slows the whole work flow down unnecessarily.

Edit due to comment further explaining the pain point: It becomes a complete mess because all the clients really need, fundamentally, is to see whether they were present, absent (with notice), absent without notice, or late. Some clients have 13 different statuses for what seems like just for the sake of it because they can and the end users who mark it end up being terribly confused as to which status to check because they end up being rather similar. It also clutters the UI unnecessarily with all these options.

As such, what we want to do is...

... standardise the attendance options for all client companies as to avoid the current situation of catering for possibly hundreds of different variations of statuses that are essentially the same in meaning. We plan to set a small yet sufficient number of available statuses and remove any option for clients to create their own statuses.

Our concern is...

... that we would face an outcry from existing customers about limiting and cutting back on the current level of customisation and control that they have over the system and that they would simply stop using the system even if they would be able to complete their work flow much easier and faster without missing anything critical.

The question at hand:

Is limiting the users ability for customisation and forcing them into standardised practices a dangerous path to take and why?

And to a further extent, how could users be persuaded to accept giving up the freedom of customisation?