Generate your sitemap.xml then prioritize them and submit it in Google webmaster Google will not index them all at once but if you have no duplicate content, title and content your fine but if ther is any thing like spam it will be as spam.
In sitemap generation it will works up to 500 pages. For your purpose try this link:
http://www.xml-sitemaps.com/standalone-google-sitemap-generator.html
There is no penalty for website with large amount of pages. In short if there is Balck hat SEO techniques it will be penalize. IMHO the above link is a good starting point for you.
Nick
