If the pointing and clicking generates code that can seen and stored, then fine. A reproducibility problem comes from the fact that most point-and-click tools don't. As a computational biologist who uses R I am often frustrated by experimental colleagues who use Excel and often can't remember how they transformed the data months later. I don't necessarily have better memory but I can go into my script and look.
In scripting languages, writing and sharing a new function isn't hard. And, if the language is open source, that encourages the rapid development of a community which implements useful and state-of-the-art tools.
If every tool needs to be available through a GUI, then, as far as I can see, that GUI will either be a burden on creators or so generalized it's no better than tab completion.
df = read_csv(file)
df <- df %>% mutate(log_income = log(income))
# do manipulations in shiny
Shiny(df)
# click "transform" in the top right hand corner...
We have had few point&click text-based systems in the past, notably Plan9 and Xerox Alto and only the letter have a complete "user friendly graphic programming environment"... I think a simpler approach like org-mode/org-babel is the best we have now out of the box.