If you feel somewhat guilty when killing bugs, your heart is in the right place. God created the universe for our sake, and He placed His creation under our dominion. A good steward cares for that which is in his care, and this includes uprooting weeds in the garden when necessary. Personally, I'm terrorized by mosquitoes. If one preys on me outdoors, I can accept that reality—weeds naturally grow in the wilderness. But if one finds itself in the confines of my house, in my garden? Well, it's gloves-off and time for business. Or, to keep up the analogy, I put on the gardening gloves and do the dirty work. If the job was successful, I thank God, but I also ask for His forgiveness, because the death of the pest in question was a direct consequence of my great weakness.
This was something that really 'bugged' me for the longest time, but my priest answered me with the weeds-in-the-garden analogy, which helped put my heart at ease.