No, they cannot be avoided. Not even on phone lines, which can take a couple hours, also guide data will not be downloaded when you have an update pending.
With the newer Roamio, there is no modem, only network, so updates only takes about 10-15 minutes and does not interrupt anything else on the network.
Series 2 (PLS, sold)
TiVo HD 1TB (157 HD Hrs, PLS, "652")
Roamio! Oh, wait, Its Juliet!
OTA! OTA! OTA!
The TiVo Apocalypse begins on Sat 2013 Feb 16 00:00 GMT!