The best way is to "test" the acutal drive yourself.
The traffic going south of San Jose to Morgan Hill and Gilroy in the afternoons is in my opinion horrendous.
You need to drive it your self to see.
I had a good friend and client who worked in Cupertino and lived in San Martin - a small town between Gilroy and Morgan Hill and she hated the drive home.
It looks to me like the traffic headed south of 101 starts to get very heavy around so if you can arrange a 6AM to 3PM work schedule the commute might be reasonable.
But before you move there, make the drive at 5PM and see for yourself.
Property values are high on the SF Peninsula becuase the commutes are reasonable to Silicon Valley employment and SF.
As my my grandma used to say "there is no free lunch" and "you get what you pay for".
Prices are lower in Morgan Hill and Gilroy than on the SF Peninsula and the longer commute is one of the main reasons.
Both locations are reasonable.
If you click on the weblink located below it will take you to a “Morgan Hill to San Jose” Google map that estimates a 25 -30 minute commute (may or may not really be possible during YOUR commute time).
You can do the same with Gilroy or any other town you want to "test drive."
EVEN BETTER, if you click on the "Traffic" button you will get real-time traffic; however, to see statistical commute times click on the "change" link right next to where it says "Live Traffic." Next, click the "Traffic at day and time" button and enter the times you want to check for your likely commute time based and historical traffic data!