He’s been with us from the beginning.
Is there a difference between from and since in the context of the quoted sentence?
I think from the beginning puts a little more emphasis and focus on the significance of the beginning. If you were talking about a business, perhaps "he" was there in the planning process and integral to starting the business. Since the beginning places more emphasis on the intervening time period. Again, if a business, perhaps "he" is the most loyal employee who was hired early on—the focus being more on the amount of time that has passed.
Beyond this, if you use the blockquoted form you'll be in better company: