Yes, it will be fine.
As a little more information (and forgive me if I'm being too basic here):
The way traffic on the internet makes its way to you is via a system called DNS (the Domain Name System, but you don't need to know that). Think of DNS like an old school phone book. You might be old enough to remember that phone books usually contained two pieces of information for each person: their phone number and their mailing address. DNS works much the same way. Like that phone book entry, each entry in DNS can contain a few different parts. The DNS "A record" tells the other computers on the internet where to find your website, and the DNS "MX record" (for "Mail eXchange") tells them where to send email for you.
So, when you're setting up Workspace, Google is asking to update your MX records in DNS, so that they can handle the email receiving and sending duties for your domain. Going back to our analogy, think of Google sorta like a UPS Store, where they have mailboxes for lots of different folks. But updating your MX records in DNS doesn't affect your A record, so your website will continue to work uninterrupted.
Hope that makes sense, and helps,
Ian
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