As commented elsewhere, I too think you probably have a dataset that is best formatted as panel data. However, I address first the specific problem I think you have according to your question. Then I show some code in case you are interested in switching to a panel structure.
Here is an example CSV file open as a spreadsheet:

And here the same file, open in a text editor. Imagine the ; are ,. This is related to my system's language settings.

Running this (substitute delimiter(";") for comma, in your case):
clear all
set more off
insheet using "D:\xlsdates.csv", delimiter(";")
results in

which I think is the problem you describe: dates as variable labels. You would like to have the dates as variable names. One solution is to use a loop and strtoname() to rename the variables based on the variable labels. The following goes after importing with insheet:
foreach var of varlist * {
local j = "`: variable l `var''"
local newname = strtoname("`j'", 1)
rename `var' `newname'
}
The result is

The function strtoname() will substitute out the ilegal characters for _'s. See help strtoname.
Now, if you want to work with a panel structure, one way would be:
clear all
set more off
insheet using "D:\xlsdates.csv", delimiter(";")
* Rename variables
foreach var of varlist * {
local j = "`: variable l `var''"
local newname = strtoname("`j'", 1)
rename `var' `newname'
}
* Generate ID
generate id = _n
* Change to long format
reshape long _, i(id) j(dat) string
* Sensible name
rename _ metric
* Generate new date variable
gen dat2 = date(dat,"DMY", 2050)
format dat2 %d
list, sepby(id)
As you can see, there's no need to do anything beforehand in Excel or in an editor. Stata seems to be enough in this case.
Note: I've reused code from http://www.stata.com/statalist/archive/2008-09/msg01316.html.
A further note on performance: A CSV file with 122 variables or days (columns) and 10,000 observations or subjects (rows) + 1 header row, will produce 1,220,000 observations after the reshape. I have tested this on some old machine with a 1.79 GHz AMD processor and 640 MB RAM and the reshape takes approximately 8 minutes. Stata 12 has a hard-limit of 2,147,483,647 observations (although available RAM determines if you can actually achieve it) and Stata SE of 32,767 variables.
reshapecommand. 3 months creates 2741784 observations and although I have read that stata/se has the capability to store unlimited observations, I'm guessing I may not have the computing power to do so? - Marko