How to set R to default options?

Like @chl said, you can save your default options somewhere, e.g. in an Rdata file using save:

default_options = options()
save(default_options, file = "default_options.rda")

Now you can load those defaults from the file and apply them:

load("default_options.rda")
options(default_options)

However, I would advice against running R scripts serially. In stead, if you have shared functionality between scripts, simply create functions that capture that functionality. The script you work in is then always self-contained, no influence from other, previously run scripts. Any options you set are then local to that script, and there is no need to empty your workspace or set your options to default.

Note that I also never save my working environment, I always reconstruct my environment using the raw data and scripts that transform that raw data. If there are parts that take a lot of time, I put them in a separate script which at the end save an Rdata file using save. I then load them in the main script using load.