Actually yes. The intent is to increase the enjoyment level of all players to result in increased revenue and higher player retention. The number of guilds that kick people out once they reach 100 should be something monitored to see if it will be common in the event the change was made permanent. Mere speculation at this point doesn't help anyone because there is currently no real data to work with.
All we have right now in measurable metrics is the number of guilds at 95-100 and their guild size. If the number of large guilds at 95-100 outnumber the small guilds at 95-100 then the current size bonus will need to be re-evaluated and boosted up.
If with this change increases the number of large guilds at 95-100 over that of the current small guilds at 95-100. That should prove that large guilds are the only ones benefiting from this change. If large guilds are rapidly hitting the 3 level cap after this change, per the concern, that can be measured and addressed. Should large guilds not be affected outside of a slow progression to next level, this also can be measured. If small guilds under a certain size is not progressing in the manner of the guild the next tier up, that can be monitored and addressed.