Can't we use google transliteration plugin with jetpack comments?

You can customize the Comment prompt under Settings > Discussion in your dashboard. You should be able to use different languages there.

You can’t, however, customize the different comment fields within the form: the language of the form depends on the language of your site, as defined in your wp-config.php file:
http://codex.wordpress.org/WordPress_in_Your_Language

While I’m not familiar with Google Translation plugins, I believe that you should be able to translate the comments once they have been published: Jetpack Comments doesn’t have any effect on the display of your comments, so you are able to customize them.

1) I’m not able to find the ‘languages’ option in settings>discussion.

Jetpack doesn’t offer such option, but allows you to specify a custom Comment prompt:
http://i.wpne.ws/NAHt

If the Google Transliteration doesn’t offer any option to translate that comment prompt, I’m afraid you will have to ask for help from the plugin author.

2) I’m talking about this service.
http://www.google.com/inputtools/cloud/try/ and this plugin http://wordpress.org/extend/plugins/google-transliteration/

You won’t be able to hook the Transliteration tool to the Jetpack Comment form, since it is not hosted on your blog It is in fact hosted on WordPress.com and added to your site via an iFrame. If you want your readers to be able to use the tool when commenting, I am afraid you will have to deactivate Jetpack Comments.

You can find out how to deactivate a Jetpack module here:
http://jetpack.me/support/#turn-off-jetpack-modules