I use Family Tree Maker which always tries to get me to accept "USA" in a place name regardless of the time of the event. Why would such a widely-used program "insist" on this method of data entry unless is is acceptable? I strip off the USA and "Ignore" the program's correction. Antiquarian place names (eg. Massachusetts Bay Colony) are not even in the database. Help me sleep better by affirming my thinking.
I've hit a similar issue (mine in Nova Scotia, and the state of Canada through time). I'm using an older (pre-Ancestry) version of Family Tree Maker for the very reason that it doesn't try to force such things on me.
To answer the unspoken question, I think you're completely correct to do what you've been doing - fighting the software's attempt to force a naming scheme on you. You know better, even if it doesn't. By maintaining the proper names through time, it helps those reading your data to have a better sense of their journey back and forth through time, as the environment changes around the individuals in your research.
It is this restriction that has led myself and other genealogical software developers to work on systems that are more aware of place naming schemes, to better support name changes through time and hierarchical changes through border changes. I'm sorry such tools aren't yet in our hands.