Many RTC chips protect against this in the hardware. For example, from the DS1307 datasheet:
When reading or writing the time and date registers, secondary (user) buffers are used to prevent errors when the
internal registers update. When reading the time and date registers, the user buffers are synchronized to the
internal registers on any I2C START. The time information is read from these secondary registers while the clock
continues to run. This eliminates the need to re-read the registers in case the internal registers update during a
read. The divider chain is reset whenever the seconds register is written. Write transfers occur on the I2C
acknowledge from the DS1307. Once the divider chain is reset, to avoid rollover issues, the remaining time and
date registers must be written within one second.