We have a site registered with the Google Webmaster Tools, but recently due to some problems we have to shutdown the site temporary. As as a result, links indexed by the Google are becoming invalid.
I want to know is it safe to delete the site from Google Webmaster Tools temporary and then re-enter the site when we start it again. Will Google crawl it again once we delete the site from it?
To directly answer the question "is it safe to delete site from Google Webmaster Tools" the short answer is yes it is safe to do.
The longer answer is removing or deactivating your account with webmasters tools won't stop Google spidering and indexing your content.
If anything I would suggest its worth having the Webmasters Tools account open as you can request a re-indexing as soon as you are ready, when one of my sites was hacked and Chrome/Firefox were displaying the big scary warning messages, I requested a re-index following a clean up, it was completed and the warning message removed in under 8 hours.
I don't see the need for removing it from Webmaster Tools, you can just say reindex.
I think you could do is similar to what Elliot Jay Stocks did a while back, which was (and this first part is optional) turn the site from a whole site into just one page to clear our pharmahacks, waited about a month, than rereleased the old version.
In that month, Google reindexed the page and said hey, it's no longer pharmahacked in searches.
As people already said in answers above; Google does not stop indexing your site even if you remove it from Webmasters Tools.
One thing you can do here just don't allow Google reading your site through Robots.txt file.
By using Robots.txt you need not to alter anything in Wtools. It will show errors for sometime in Wtools; which will generally go.
